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https://github.com/galaxyproject/galaxy.git
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Added functional tests for sniffing and metadata settings on file upload. Fixed a test in the 'Filter Maf Blocks by size' tool. Added new test data. Commited the bug fix I really wanted in Axt.sniff().
This commit is contained in:
Greg Von Kuster
@@ -164,21 +164,20 @@ class Axt( Alignment ):
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headers = get_headers( filename, None )
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if len(headers) < 4:
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return False
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for line_list in headers:
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if len(line_list) > 0:
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line = line_list[0]
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if line and line.startswith("##matrix=axt"):
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for hdr in headers:
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if len(hdr) > 0 and hdr[0].startswith("##matrix=axt"):
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return True
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if len(hdr) > 0 and not hdr[0].startswith("#"):
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if len(hdr) != 9:
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return False
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try:
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map ( int, [hdr[0], hdr[2], hdr[3], hdr[5], hdr[6], hdr[8]] )
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except:
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return False
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if hdr[7] not in data.valid_strand:
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return False
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else:
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return True
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if line and not line.startswith("#"):
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if len(line) != 9:
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return False
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try:
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map ( int, [line[0], line[2], line[3], line[5], line[6], line[8]] )
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except:
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return False
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if line[7] not in data.valid_strand:
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return False
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return True
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class Lav( Alignment ):
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"""Class describing a LAV alignment"""
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@@ -13,7 +13,7 @@ elif [ $1 = 'help' ]; then
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echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb'"
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echo "'run_functional_tests.sh -list' for listing all the tool ids"
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elif [ $1 = '-id' ]; then
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./nosetests.sh -v -w test functional.test_toolbox:GeneratedToolTestCase_$2 --with-nosehtml --html-report-file run_functional_tests.html
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./nosetests.sh -v -w test functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html
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elif [ $1 = '-list' ]; then
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python tool_list.py
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echo "==========================================================================================================================================="
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File diff suppressed because one or more lines are too long
+178
@@ -0,0 +1,178 @@
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#:lav
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d {
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"blastz out.seq1m seq2data Y=3400 H=0 W=8 B=2 K=3000 C=0 m=83886080 P=0
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A C G T
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91 -114 -31 -123
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-114 100 -125 -31
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-31 -125 100 -114
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-123 -31 -114 91
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O = 400, E = 30, K = 3000, L = 3000, M = 50"
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}
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#:lav
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s {
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"out.seq1m" 1 1680 0 1
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"seq2data" 1 1680 0 1
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}
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h {
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">seqmask seq1data out.repeats"
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">seq2"
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}
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a {
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s 161304
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b 1 1
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e 1680 1680
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l 1 1 1680 1680 100
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}
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a {
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s 15173
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b 186 251
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e 450 505
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l 186 251 244 309 92
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l 256 310 280 334 84
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l 281 336 307 362 78
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l 308 374 329 395 91
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l 341 396 367 422 81
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l 369 423 419 473 94
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l 422 474 425 477 75
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l 426 481 450 505 96
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}
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a {
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s 12134
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b 191 343
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e 361 503
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l 191 343 215 367 80
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l 216 369 244 397 86
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l 256 398 361 503 95
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}
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a {
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s 4422
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b 192 431
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e 276 505
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l 192 431 212 451 100
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l 223 452 244 473 95
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l 247 474 254 481 63
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l 255 484 276 505 91
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}
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a {
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s 6872
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b 192 311
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e 330 450
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l 192 311 215 334 83
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l 216 336 275 395 73
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l 286 396 307 417 91
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l 308 428 330 450 96
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}
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a {
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s 14437
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b 192 224
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e 472 505
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l 192 224 223 255 84
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l 224 257 255 288 84
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l 257 289 277 309 90
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l 288 310 308 330 90
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l 309 342 362 395 85
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l 374 396 395 417 91
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l 396 428 417 449 95
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l 428 450 449 471 95
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l 450 483 472 505 91
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}
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a {
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s 7306
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b 192 399
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e 308 505
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l 192 399 244 451 94
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l 256 452 277 473 91
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l 280 474 283 477 100
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l 284 481 308 505 92
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}
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a {
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s 11180
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b 193 290
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e 396 505
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l 193 290 212 309 100
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l 223 310 280 367 76
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l 281 369 332 420 88
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l 333 422 335 424 100
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l 336 429 341 434 83
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l 342 451 396 505 87
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}
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a {
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s 14437
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b 224 192
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e 505 472
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l 224 192 255 223 84
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l 257 224 288 255 84
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l 289 257 309 277 90
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l 310 288 330 308 90
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l 342 309 395 362 85
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l 396 374 417 395 91
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l 428 396 449 417 95
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l 450 428 471 449 95
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l 483 450 505 472 91
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}
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a {
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s 15173
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b 251 186
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e 505 450
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l 251 186 309 244 92
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l 310 256 334 280 84
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l 336 281 362 307 78
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l 374 308 395 329 91
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l 396 341 422 367 81
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l 423 369 473 419 94
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l 474 422 477 425 75
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l 481 426 505 450 96
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}
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a {
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s 11180
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b 290 193
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e 505 396
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l 290 193 309 212 100
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l 310 223 367 280 76
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l 369 281 420 332 88
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l 422 333 424 335 100
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l 429 336 434 341 83
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l 451 342 505 396 87
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}
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a {
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s 6872
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b 311 192
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e 450 330
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l 311 192 334 215 83
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l 336 216 395 275 73
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l 396 286 417 307 91
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l 428 308 450 330 96
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}
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a {
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s 12134
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b 343 191
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e 503 361
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l 343 191 367 215 80
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l 369 216 397 244 86
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l 398 256 503 361 95
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}
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a {
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s 7306
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b 399 192
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e 505 308
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l 399 192 451 244 94
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l 452 256 473 277 91
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l 474 280 477 283 100
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l 481 284 505 308 92
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}
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a {
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s 4422
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b 431 192
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e 505 276
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l 431 192 451 212 100
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l 452 223 473 244 95
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l 474 247 481 254 63
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l 484 255 505 276 91
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}
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x {
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n 0
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}
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m {
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n 0
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}
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#:eof
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@@ -0,0 +1,3 @@
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track type=wiggle_0 name="tb_knownGene" description="table browser query on knownGene" visibility=3 url=
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chr7 127475281 127491632 NM_000230 0 + 127486022 127488767 0 3 29,172,3225, 0,10713,13126,
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chr7 127486011 127488900 D49487 0 + 127486022 127488767 0 2 155,490, 0,2399,
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+36
-36
@@ -1,55 +1,55 @@
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##maf version=1
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a score=60426.0
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s hg17.chr7 127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
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s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
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s mm5.chr6 28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA
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s rn3.chr4 56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA
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s hg17.chr7 127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
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s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
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s mm5.chr6 28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA
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s rn3.chr4 56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA
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a score=8157.0
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s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
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s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
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s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG
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s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
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s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
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s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG
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a score=43613.0
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s hg17.chr7 127471584 104 + 158628139 GAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt
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s panTro1.chr6 129885465 104 + 161576975 GAGACATTTGGggaaatt---ttgtatagactagctttcacgatgttagggagttattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt
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s mm5.chr6 28909125 102 + 149721531 GAGACATTTGGGGGAAATACGATGTATA------CTTTCATGATCTTAAAGAATTGCTATTGTTTGATAGTGATATTATGGTTAAATTAAAAAAAAACCCTTACTTTT
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s rn3.chr4 56182196 99 + 187371129 GAGATATTTGGGGGAAATATGATGTGCA------CTTCCATGATCTTAAAGAATTGCTACTGTTTGATAGTGATCTTATGGTTAAA-TAAAAAAAAT--CTTAGTTGT
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s canFam1.chr14 52864846 108 - 63549963 GAGATATTTGGGGGAATTTGAATGTAGTGTTGCTCTTTTGTGATGCTAAGAAATTATAATTGTCTGATGATAGTCTCGTGGTTATGGGGGAAATGCTTCCTTATTTTT
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s hg17.chr7 127471584 104 + 158628139 GAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt
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s panTro1.chr6 129885465 104 + 161576975 GAGACATTTGGggaaatt---ttgtatagactagctttcacgatgttagggagttattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt
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s mm5.chr6 28909125 102 + 149721531 GAGACATTTGGGGGAAATACGATGTATA------CTTTCATGATCTTAAAGAATTGCTATTGTTTGATAGTGATATTATGGTTAAATTAAAAAAAAACCCTTACTTTT
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s rn3.chr4 56182196 99 + 187371129 GAGATATTTGGGGGAAATATGATGTGCA------CTTCCATGATCTTAAAGAATTGCTACTGTTTGATAGTGATCTTATGGTTAAA-TAAAAAAAAT--CTTAGTTGT
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s canFam1.chr14 52864846 108 - 63549963 GAGATATTTGGGGGAATTTGAATGTAGTGTTGCTCTTTTGTGATGCTAAGAAATTATAATTGTCTGATGATAGTCTCGTGGTTATGGGGGAAATGCTTCCTTATTTTT
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a score=63217.0
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s hg17.chr7 127471688 183 + 158628139 tgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaa
|
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s panTro1.chr6 129885569 183 + 161576975 tgggaa---acaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacgctttaaaatatttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaaattttcatttaaaaa
|
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s mm5.chr6 28909227 176 + 149721531 CATAAA---ATACTCAAATATTTAGGGGTATGACAATGTCATAGTGTCTGCAATTTGCTTTAAAATAATTTTG-------AAAAC---------------------CTGAGGCTAAACTATGGGAA-ATAGCAATTATTACATATGGGTAATAAGTA-----TAACTCACTATATTATTTTTCACTAT----TGTGTTTGAAATTTTCATTTTAAAA
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s rn3.chr4 56182295 194 + 187371129 TAGAAA---ATACTCAAATATTTAGGGGCGTGACAATGTCACAGTGTCTGCAATTTGCTTTAAAG-ATTTTTAAATATTTAAAAAAGTTTTAATAATTTTGAAAAACTGAAGCTACACTATGGGAA-GTGGTAATTGTTACATATGGGTAATAAGTA-----TAATTCGTTATATTATT-------------TTTCTTAGAATTTTTCATTTGAAAA
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s canFam1.chr14 52865149 163 - 63549963 tagagacacaaactgaagtatttaaggat---gaaatgtcatgatgtttgcaattggctttaaaatattttag-----ccaaaa-agta----------------aatgaagc--aaatatgggaagacaataatcattaaatctaggtgaTGCATA---------------------------CTTTTCCATATGTTTGAAATTTTCATTTAAAAA
|
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s hg17.chr7 127471688 183 + 158628139 tgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaa
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s panTro1.chr6 129885569 183 + 161576975 tgggaa---acaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacgctttaaaatatttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaaattttcatttaaaaa
|
||||
s mm5.chr6 28909227 176 + 149721531 CATAAA---ATACTCAAATATTTAGGGGTATGACAATGTCATAGTGTCTGCAATTTGCTTTAAAATAATTTTG-------AAAAC---------------------CTGAGGCTAAACTATGGGAA-ATAGCAATTATTACATATGGGTAATAAGTA-----TAACTCACTATATTATTTTTCACTAT----TGTGTTTGAAATTTTCATTTTAAAA
|
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s rn3.chr4 56182295 194 + 187371129 TAGAAA---ATACTCAAATATTTAGGGGCGTGACAATGTCACAGTGTCTGCAATTTGCTTTAAAG-ATTTTTAAATATTTAAAAAAGTTTTAATAATTTTGAAAAACTGAAGCTACACTATGGGAA-GTGGTAATTGTTACATATGGGTAATAAGTA-----TAATTCGTTATATTATT-------------TTTCTTAGAATTTTTCATTTGAAAA
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s canFam1.chr14 52865149 163 - 63549963 tagagacacaaactgaagtatttaaggat---gaaatgtcatgatgtttgcaattggctttaaaatattttag-----ccaaaa-agta----------------aatgaagc--aaatatgggaagacaataatcattaaatctaggtgaTGCATA---------------------------CTTTTCCATATGTTTGAAATTTTCATTTAAAAA
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||||
|
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a score=8913.0
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s hg17.chr7 127471872 40 + 158628139 ctttgagc-----tagacaccaggctatgagctaggagcatagca
|
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s panTro1.chr6 129885753 40 + 161576975 ctttgagc-----tagacaccaggctatgagctaggagcatagca
|
||||
s mm5.chr6 28910662 44 + 149721531 CTTTGTGCTTAGGTAGGCACTGAGCTCTTAAATTGGA-TACAGCG
|
||||
s canFam1.chr14 52865538 40 - 63549963 CATCAtgc-----tagatcctggactatgagctgggtatatagca
|
||||
s hg17.chr7 127471872 40 + 158628139 ctttgagc-----tagacaccaggctatgagctaggagcatagca
|
||||
s panTro1.chr6 129885753 40 + 161576975 ctttgagc-----tagacaccaggctatgagctaggagcatagca
|
||||
s mm5.chr6 28910662 44 + 149721531 CTTTGTGCTTAGGTAGGCACTGAGCTCTTAAATTGGA-TACAGCG
|
||||
s canFam1.chr14 52865538 40 - 63549963 CATCAtgc-----tagatcctggactatgagctgggtatatagca
|
||||
|
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a score=91878.0
|
||||
s hg17.chr7 127471912 335 + 158628139 atgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccggga
|
||||
s panTro1.chr6 129885793 335 + 161576975 atgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaatttttcctg-ggcacccatgtgttcttggcactggaaaagtaccggga
|
||||
s mm5.chr6 28910706 350 + 149721531 ATGAGCAA----------------------------------------------------------------------------------------------AAAAACAACAACAAAAAACAAACAAACAAAAAAACCAAAAACCAAAAACCAAAAAAACCTATAGCCTC-ACAGGGTGGGTTGTCTTTGAGGAACATGCATCCGCTAGAAAGTCCCAAGTACACTATGACAGTTG--CCCAGGCCCCGCCTTAAACCTGGTTTTCCTGGTTTCTTTCA---CATCATTACCACGAATATATTTCCTCAAGTTTAAAGAAAGTACCCCCTCCTTTCCAGT-GCCTCAAATCTAGAAGAATATTCATAGTGAAGT-GCA------------------------CAGCCGGGTGGTGCATGGTAAT-CTGGAAGTCACCTCTGCAAATCTTTCCTG----------------TTGGTGCTGTGAAGGCACCAGGA
|
||||
s rn3.chr4 56183448 420 + 187371129 ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTTGTGCTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC--------------------------------------------------CTC-ACAGGGTGGGTTGTCTTTGAGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGGTTTAAAAGAAGTC-CCACTCCTTTCCAGT-GCCCTAGATCTAGAAGCACATTCATAATGATGT-ACACTAACCCGA---------------CAGCTGTGTGGTATATGGTATC-CCGGAAGTCACCTCAGCAAACCTTTCCCGGGGAACCTACATGGTGTTGGTGCTGTGAAGGTACCAGGT
|
||||
s canFam1.chr14 52865578 336 - 63549963 gtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt--------------------------------------------------cttgatggagcacacaACCTTTGGGGAACATGTTTCCATAAGAAAGTCTCCAATGTGATCTGATGGT-GCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACATTTTAAATATCTG-------CTTCCCGGTGGCCTTGAGTCTAGAGGAGTCCCCCCACTATGGTGGCACTAATACTGAAGGTCAGAAATAATCAGTTCTGTGGTGCATGTTGCCCCTGAGGTTCTGTTCGGGAAACTTCTTCTG-AGCAC----ATGCACCTGGCACTGCAAACGTACCAGGA
|
||||
s hg17.chr7 127471912 335 + 158628139 atgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccggga
|
||||
s panTro1.chr6 129885793 335 + 161576975 atgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaatttttcctg-ggcacccatgtgttcttggcactggaaaagtaccggga
|
||||
s mm5.chr6 28910706 350 + 149721531 ATGAGCAA----------------------------------------------------------------------------------------------AAAAACAACAACAAAAAACAAACAAACAAAAAAACCAAAAACCAAAAACCAAAAAAACCTATAGCCTC-ACAGGGTGGGTTGTCTTTGAGGAACATGCATCCGCTAGAAAGTCCCAAGTACACTATGACAGTTG--CCCAGGCCCCGCCTTAAACCTGGTTTTCCTGGTTTCTTTCA---CATCATTACCACGAATATATTTCCTCAAGTTTAAAGAAAGTACCCCCTCCTTTCCAGT-GCCTCAAATCTAGAAGAATATTCATAGTGAAGT-GCA------------------------CAGCCGGGTGGTGCATGGTAAT-CTGGAAGTCACCTCTGCAAATCTTTCCTG----------------TTGGTGCTGTGAAGGCACCAGGA
|
||||
s rn3.chr4 56183448 420 + 187371129 ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTTGTGCTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC--------------------------------------------------CTC-ACAGGGTGGGTTGTCTTTGAGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGGTTTAAAAGAAGTC-CCACTCCTTTCCAGT-GCCCTAGATCTAGAAGCACATTCATAATGATGT-ACACTAACCCGA---------------CAGCTGTGTGGTATATGGTATC-CCGGAAGTCACCTCAGCAAACCTTTCCCGGGGAACCTACATGGTGTTGGTGCTGTGAAGGTACCAGGT
|
||||
s canFam1.chr14 52865578 336 - 63549963 gtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt--------------------------------------------------cttgatggagcacacaACCTTTGGGGAACATGTTTCCATAAGAAAGTCTCCAATGTGATCTGATGGT-GCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACATTTTAAATATCTG-------CTTCCCGGTGGCCTTGAGTCTAGAGGAGTCCCCCCACTATGGTGGCACTAATACTGAAGGTCAGAAATAATCAGTTCTGTGGTGCATGTTGCCCCTGAGGTTCTGTTCGGGAAACTTCTTCTG-AGCAC----ATGCACCTGGCACTGCAAACGTACCAGGA
|
||||
|
||||
a score=82819.0
|
||||
s hg17.chr7 127472258 423 + 158628139 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgt
|
||||
s panTro1.chr6 129886139 423 + 161576975 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGACCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgtaaatttcctgt
|
||||
s mm5.chr6 28911067 334 + 149721531 AATGGCAGAGGGCTCTGTTCTCT----------------------------------GTCCA---TAGACAAGGAAGC---------CTGCCAGTGG-----------------------TGGAGAGCAGGGCCTATGCAAAACAGGGGGGGTTCTGTGGGCAGAAGGGATGGACCTGACTCCAGGAACGCCCATA-AGAGACGGGCAGGACTGGGAGCCAGGAGCAGCCAGCGCA--------GGTGTGTGTAGGTTTCATAGTTT---------------------------GCAGGTTAGCAAACAATTCTCGCTTGGCAGGCCAAGA-GGGAAAT-AAAGGTTACCCCGTGGGTACTTAT---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTTAATTTCTTAA
|
||||
s rn3.chr4 56183879 340 + 187371129 AATGGCAGAGGCCCCTGTTCTCT----------------------------------GTCCA---TAGTCAAAGAAGC---------CTCTCAG----------------------A---TGGAGAGCAGGGCCTATGCAAAAG-AGGGGGCTTCTGTAGGCAGAAGGGATGGACTAGCCTCCGGACATAGCCATAGAGAGGCTGGCAGGACTGAGACCCAGGAGAAGCCAGCGCAGGTGTGCGGGCGTGTGTATATTTCATAGTTT---------------------------GCAGGTTGGCAAACAATTCCTGCTTTGCAGGCCAAGA-GGAAACT-GAAGGTGACCCCGTGAGTGCTTAC---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTAAATTTCTTTT
|
||||
s canFam1.chr14 52866108 405 - 63549963 GGAGACTTG-ATGCCTGCCTTCCACTTACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAGAAGAGACCCC---------GG--------TGCTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTAACGTG-------CAATGTA------TTTTCTAGTTCCAgggttggcaaactttctctctaagggtgggatgataaacattttaggcttttcagaccaagaggcgacatcagagggtat---gtaggt---------acaagagggaaaagttgcccccggaattttttg--gataaaattcaaaactttacttagggatgccaaaatgtaaacttcatat
|
||||
s hg17.chr7 127472258 423 + 158628139 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgt
|
||||
s panTro1.chr6 129886139 423 + 161576975 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGACCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgtaaatttcctgt
|
||||
s mm5.chr6 28911067 334 + 149721531 AATGGCAGAGGGCTCTGTTCTCT----------------------------------GTCCA---TAGACAAGGAAGC---------CTGCCAGTGG-----------------------TGGAGAGCAGGGCCTATGCAAAACAGGGGGGGTTCTGTGGGCAGAAGGGATGGACCTGACTCCAGGAACGCCCATA-AGAGACGGGCAGGACTGGGAGCCAGGAGCAGCCAGCGCA--------GGTGTGTGTAGGTTTCATAGTTT---------------------------GCAGGTTAGCAAACAATTCTCGCTTGGCAGGCCAAGA-GGGAAAT-AAAGGTTACCCCGTGGGTACTTAT---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTTAATTTCTTAA
|
||||
s rn3.chr4 56183879 340 + 187371129 AATGGCAGAGGCCCCTGTTCTCT----------------------------------GTCCA---TAGTCAAAGAAGC---------CTCTCAG----------------------A---TGGAGAGCAGGGCCTATGCAAAAG-AGGGGGCTTCTGTAGGCAGAAGGGATGGACTAGCCTCCGGACATAGCCATAGAGAGGCTGGCAGGACTGAGACCCAGGAGAAGCCAGCGCAGGTGTGCGGGCGTGTGTATATTTCATAGTTT---------------------------GCAGGTTGGCAAACAATTCCTGCTTTGCAGGCCAAGA-GGAAACT-GAAGGTGACCCCGTGAGTGCTTAC---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTAAATTTCTTTT
|
||||
s canFam1.chr14 52866108 405 - 63549963 GGAGACTTG-ATGCCTGCCTTCCACTTACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAGAAGAGACCCC---------GG--------TGCTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTAACGTG-------CAATGTA------TTTTCTAGTTCCAgggttggcaaactttctctctaagggtgggatgataaacattttaggcttttcagaccaagaggcgacatcagagggtat---gtaggt---------acaagagggaaaagttgcccccggaattttttg--gataaaattcaaaactttacttagggatgccaaaatgtaaacttcatat
|
||||
|
||||
a score=15522.0
|
||||
s hg17.chr7 127473809 97 + 158628139 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgc
|
||||
s panTro1.chr6 129887686 97 + 161576975 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-AAGGCTCGGTTCACCAACATCATTTGC
|
||||
s canFam1.chr14 52866548 97 - 63549963 tatatttttcaactctttaaaaatgcaaaaaccattcctagc-tcggggccatggtggtcctggtggtggtcggatttggctcacccacataacttgc
|
||||
s hg17.chr7 127473809 97 + 158628139 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgc
|
||||
s panTro1.chr6 129887686 97 + 161576975 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-AAGGCTCGGTTCACCAACATCATTTGC
|
||||
s canFam1.chr14 52866548 97 - 63549963 tatatttttcaactctttaaaaatgcaaaaaccattcctagc-tcggggccatggtggtcctggtggtggtcggatttggctcacccacataacttgc
|
||||
|
||||
a score=28088.0
|
||||
s hg17.chr7 127473906 331 + 158628139 agttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct
|
||||
s panTro1.chr6 129887783 318 + 161576975 AGTTCCCCGCTTTATATTATGGGttttttttttttttttttttttttattgagacagagtttcactcttgttgcccaggctgtagtg--------------tggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcatcatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct
|
||||
s hg17.chr7 127473906 331 + 158628139 agttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct
|
||||
s panTro1.chr6 129887783 318 + 161576975 AGTTCCCCGCTTTATATTATGGGttttttttttttttttttttttttattgagacagagtttcactcttgttgcccaggctgtagtg--------------tggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcatcatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct
|
||||
|
||||
|
||||
+4
-4
@@ -1,7 +1,7 @@
|
||||
## gff-version 2
|
||||
## Date: Thu Mar 23 11:21:17 2006
|
||||
## bed2gff.pl $Rev: 601 $
|
||||
## Input file: ./database/files/61c6c604e0ef50b280e2fd9f1aa7da61.dat
|
||||
##gff-version 2
|
||||
##Date: Thu Mar 23 11:21:17 2006
|
||||
##bed2gff.pl $Rev: 601 $
|
||||
##Input file: ./database/files/61c6c604e0ef50b280e2fd9f1aa7da61.dat
|
||||
|
||||
chr1 bed2gff CCDS1000.1_cds_0_0_chr1_148325916_f 148325916 148325975 . + . score "0";
|
||||
chr2 bed2gff CCDS2120.1_cds_0_0_chr2_118288584_f 118288584 118288668 . + . score "0";
|
||||
|
||||
@@ -0,0 +1,150 @@
|
||||
##gff-version 3
|
||||
##date Tue Jun 26 10:48:17 2007
|
||||
##sequence-region ctgA 1 50000
|
||||
##source gbrowse GFFToGalaxyDumper plugin
|
||||
##NOTE: All features dumped.
|
||||
ctgA example my_feature 22132 24633 . + . ID=My_feature:f15
|
||||
ctgA example my_feature 46990 48410 . - . ID=My_feature:f11
|
||||
ctgA example my_feature 44705 47713 . - . ID=My_feature:f01
|
||||
ctgA example my_feature 36649 40440 . - . ID=My_feature:f03
|
||||
ctgA example my_feature 23072 23185 . + . ID=My_feature:f14
|
||||
ctgA example my_feature 37242 38653 . + . ID=My_feature:f04
|
||||
ctgA example motif 37497 40559 . - . ID=Motif:m15;Note=7-transmembrane
|
||||
ctgA example my_feature 36034 38167 . + . ID=My_feature:f09
|
||||
ctgA example motif 28332 30033 . - . ID=Motif:m02;Note=HOX
|
||||
ctgA example my_feature 4715 5968 . - . ID=My_feature:f05
|
||||
ctgA example motif 48253 48366 . + . ID=Motif:m01;Note=WD40
|
||||
ctgA example BAC 1000 20000 . . . ID=BAC:b101.2;Note=Fingerprinted+BAC+with+end+reads
|
||||
ctgA example right_end_read 19500 20000 . - . Parent=BAC:b101.2
|
||||
ctgA example left_end_read 1000 1500 . + . Parent=BAC:b101.2
|
||||
ctgA example motif 13801 14007 . - . ID=Motif:m05;Note=helix+loop+helix
|
||||
ctgA example coding 1050 9000 . + . ID=mRNA:EDEN.1;Gene=EDEN
|
||||
ctgA example CDS 1201 1500 . + 0 Parent=mRNA:EDEN.1
|
||||
ctgA example CDS 3000 3902 . + 0 Parent=mRNA:EDEN.1
|
||||
ctgA example CDS 5000 5500 . + 0 Parent=mRNA:EDEN.1
|
||||
ctgA example CDS 7000 7608 . + 0 Parent=mRNA:EDEN.1
|
||||
ctgA example processed_transcript 1050 9000 . + . ID=mRNA:EDEN.1
|
||||
ctgA example 5'-UTR 1050 1200 . + . Parent=mRNA:EDEN.1
|
||||
ctgA example 3'-UTR 7609 9000 . + . Parent=mRNA:EDEN.1
|
||||
ctgA est match 5410 7503 . - . ID=EST:agt830.3;Target=agt830.3+1+595
|
||||
ctgA est HSP 7000 7503 . - . Parent=EST:agt830.3;Target=agt830.3+1+504
|
||||
ctgA est HSP 5410 5500 . - . Parent=EST:agt830.3;Target=agt830.3+505+595
|
||||
ctgA example motif 46012 48851 . + . ID=Motif:m09;Note=kinase
|
||||
ctgA example match 6885 8999 . - . ID=Match:seg03
|
||||
ctgA example HSP 8306 8999 . - . Parent=Match:seg03
|
||||
ctgA example HSP 8055 8080 . - . Parent=Match:seg03
|
||||
ctgA example HSP 7410 7737 . - . Parent=Match:seg03
|
||||
ctgA example HSP 6885 7241 . - . Parent=Match:seg03
|
||||
ctgA example my_feature 13280 16394 . + . ID=My_feature:f08
|
||||
ctgA example match 29771 32937 . + . ID=Match:seg10
|
||||
ctgA example HSP 29771 29942 . + . Parent=Match:seg10
|
||||
ctgA example HSP 30042 30340 . + . Parent=Match:seg10
|
||||
ctgA example HSP 30810 31307 . + . Parent=Match:seg10
|
||||
ctgA example HSP 31761 31984 . + . Parent=Match:seg10
|
||||
ctgA example HSP 32374 32937 . + . Parent=Match:seg10
|
||||
ctgA example match 36616 37227 . - . ID=Match:seg09
|
||||
ctgA example HSP 37208 37227 . - . Parent=Match:seg09
|
||||
ctgA example HSP 36616 37057 . - . Parent=Match:seg09
|
||||
ctgA example motif 11911 15561 . + . ID=Motif:m11;Note=kinase
|
||||
ctgA est match 1050 3202 . + . ID=EST:agt830.5;Target=agt830.5+1+654
|
||||
ctgA est HSP 1050 1500 . + . Parent=EST:agt830.5;Target=agt830.5+1+451
|
||||
ctgA est HSP 3000 3202 . + . Parent=EST:agt830.5;Target=agt830.5+452+654
|
||||
ctgA example motif 15396 16159 . + . ID=Motif:m03;Note=zinc+finger
|
||||
ctgA est match 1150 7200 . + . ID=EST:agt767.5;Target=agt767.5+1+1153
|
||||
ctgA est HSP 1150 1500 . + . Parent=EST:agt767.5;Target=agt767.5+1+351
|
||||
ctgA est HSP 5000 5500 . + . Parent=EST:agt767.5;Target=agt767.5+352+852
|
||||
ctgA est HSP 7000 7200 . + . Parent=EST:agt767.5;Target=agt767.5+853+1153
|
||||
ctgA est match 1050 7300 . + . ID=EST:agt221.5;Target=agt221.5+1+1253
|
||||
ctgA est HSP 1050 1500 . + . Parent=EST:agt221.5;Target=agt221.5+1+451
|
||||
ctgA est HSP 5000 5500 . + . Parent=EST:agt221.5;Target=agt221.5+452+952
|
||||
ctgA est HSP 7000 7300 . + . Parent=EST:agt221.5;Target=agt221.5+953+1253
|
||||
ctgA example my_feature 19157 22915 . - . ID=My_feature:f13
|
||||
ctgA est match 8000 9000 . - . ID=EST:agt767.3;Target=agt767.3+1+1001
|
||||
ctgA est HSP 8000 9000 . - . Parent=EST:agt767.3;Target=agt767.3+1+1001
|
||||
ctgA example motif 28342 28447 . - . ID=Motif:m10;Note=DEAD+box
|
||||
ctgA example motif 17667 17690 . + . ID=Motif:m13;Note=DEAD+box
|
||||
ctgA example trace 44401 45925 . + . ID=name:trace;trace=volvox_trace.scf
|
||||
ctgA example match 26122 34466 . + . ID=Match:seg02
|
||||
ctgA example HSP 26122 26126 . + . Parent=Match:seg02
|
||||
ctgA example HSP 26497 26869 . + . Parent=Match:seg02
|
||||
ctgA example HSP 27201 27325 . + . Parent=Match:seg02
|
||||
ctgA example HSP 27372 27433 . + . Parent=Match:seg02
|
||||
ctgA example HSP 27565 27565 . + . Parent=Match:seg02
|
||||
ctgA example HSP 27813 28091 . + . Parent=Match:seg02
|
||||
ctgA example HSP 28093 28201 . + . Parent=Match:seg02
|
||||
ctgA example HSP 28329 28377 . + . Parent=Match:seg02
|
||||
ctgA example HSP 28829 29194 . + . Parent=Match:seg02
|
||||
ctgA example HSP 29517 29702 . + . Parent=Match:seg02
|
||||
ctgA example HSP 29713 30061 . + . Parent=Match:seg02
|
||||
ctgA example HSP 30329 30774 . + . Parent=Match:seg02
|
||||
ctgA example HSP 30808 31306 . + . Parent=Match:seg02
|
||||
ctgA example HSP 31516 31729 . + . Parent=Match:seg02
|
||||
ctgA example HSP 31753 32154 . + . Parent=Match:seg02
|
||||
ctgA example HSP 32595 32696 . + . Parent=Match:seg02
|
||||
ctgA example HSP 32892 32901 . + . Parent=Match:seg02
|
||||
ctgA example HSP 33127 33388 . + . Parent=Match:seg02
|
||||
ctgA example HSP 33439 33443 . + . Parent=Match:seg02
|
||||
ctgA example HSP 33759 34209 . + . Parent=Match:seg02
|
||||
ctgA example HSP 34401 34466 . + . Parent=Match:seg02
|
||||
ctgA example contig 1 50000 . . . ID=Contig:ctgA
|
||||
ctgA example match 41137 47829 . - . ID=Match:seg14
|
||||
ctgA example HSP 47449 47829 . - . Parent=Match:seg14
|
||||
ctgA example HSP 46816 46992 . - . Parent=Match:seg14
|
||||
ctgA example HSP 46092 46318 . - . Parent=Match:seg14
|
||||
ctgA example HSP 45790 46022 . - . Parent=Match:seg14
|
||||
ctgA example HSP 45231 45488 . - . Parent=Match:seg14
|
||||
ctgA example HSP 44763 45030 . - . Parent=Match:seg14
|
||||
ctgA example HSP 44065 44556 . - . Parent=Match:seg14
|
||||
ctgA example HSP 43395 43811 . - . Parent=Match:seg14
|
||||
ctgA example HSP 42890 43270 . - . Parent=Match:seg14
|
||||
ctgA example HSP 42057 42474 . - . Parent=Match:seg14
|
||||
ctgA example HSP 41754 41948 . - . Parent=Match:seg14
|
||||
ctgA example HSP 41137 41318 . - . Parent=Match:seg14
|
||||
ctgA example match 12531 15870 . + . ID=Match:seg12
|
||||
ctgA example HSP 12531 12895 . + . Parent=Match:seg12
|
||||
ctgA example HSP 13122 13449 . + . Parent=Match:seg12
|
||||
ctgA example HSP 13452 13745 . + . Parent=Match:seg12
|
||||
ctgA example HSP 13908 13965 . + . Parent=Match:seg12
|
||||
ctgA example HSP 13998 14488 . + . Parent=Match:seg12
|
||||
ctgA example HSP 14564 14899 . + . Parent=Match:seg12
|
||||
ctgA example HSP 15185 15276 . + . Parent=Match:seg12
|
||||
ctgA example HSP 15639 15736 . + . Parent=Match:seg12
|
||||
ctgA example HSP 15745 15870 . + . Parent=Match:seg12
|
||||
ctgA est match 7500 8000 . - . ID=EST:agt221.3;Target=agt221.3+1+501
|
||||
ctgA est HSP 7500 8000 . - . Parent=EST:agt221.3;Target=agt221.3+1+501
|
||||
ctgA example coding 1300 9000 . + . ID=mRNA:EDEN.3;Gene=EDEN
|
||||
ctgA example CDS 3301 3902 . + 0 Parent=mRNA:EDEN.3
|
||||
ctgA example CDS 5000 5500 . + 1 Parent=mRNA:EDEN.3
|
||||
ctgA example CDS 7000 7600 . + 1 Parent=mRNA:EDEN.3
|
||||
ctgA example processed_transcript 1300 9000 . + . ID=mRNA:EDEN.3
|
||||
ctgA example 5'-UTR 1300 1500 . + . Parent=mRNA:EDEN.3
|
||||
ctgA example 5'-UTR 3000 3300 . + . Parent=mRNA:EDEN.3
|
||||
ctgA example 3'-UTR 7601 9000 . + . Parent=mRNA:EDEN.3
|
||||
ctgA example match 26503 35904 . - . ID=Match:seg05
|
||||
ctgA example HSP 35642 35904 . - . Parent=Match:seg05
|
||||
ctgA example HSP 35333 35507 . - . Parent=Match:seg05
|
||||
ctgA example HSP 34605 34983 . - . Parent=Match:seg05
|
||||
ctgA example HSP 34244 34313 . - . Parent=Match:seg05
|
||||
ctgA example HSP 33438 33868 . - . Parent=Match:seg05
|
||||
ctgA example HSP 33053 33325 . - . Parent=Match:seg05
|
||||
ctgA example HSP 32208 32680 . - . Parent=Match:seg05
|
||||
ctgA example HSP 32010 32057 . - . Parent=Match:seg05
|
||||
ctgA example HSP 31421 31817 . - . Parent=Match:seg05
|
||||
ctgA example HSP 31232 31236 . - . Parent=Match:seg05
|
||||
ctgA example HSP 30465 30798 . - . Parent=Match:seg05
|
||||
ctgA example HSP 30108 30216 . - . Parent=Match:seg05
|
||||
ctgA example HSP 29513 29647 . - . Parent=Match:seg05
|
||||
ctgA example HSP 28777 29058 . - . Parent=Match:seg05
|
||||
ctgA example HSP 28225 28316 . - . Parent=Match:seg05
|
||||
ctgA example HSP 27887 28076 . - . Parent=Match:seg05
|
||||
ctgA example HSP 27448 27860 . - . Parent=Match:seg05
|
||||
ctgA example HSP 27172 27185 . - . Parent=Match:seg05
|
||||
ctgA example HSP 26503 26799 . - . Parent=Match:seg05
|
||||
ctgA example match 49406 50000 . + . ID=Match:seg13
|
||||
ctgA example HSP 49406 49476 . + . Parent=Match:seg13
|
||||
ctgA example HSP 49762 50000 . + . Parent=Match:seg13
|
||||
ctgA example gene 1050 9000 . + . ID=Gene:EDEN;Note=protein+kinase
|
||||
ctgA example motif 33325 35791 . + . ID=Motif:m04;Note=Ig-like
|
||||
ctgA example match 31785 32359 . + . ID=Match:seg01
|
||||
ctgA example HSP 31785 31939 . + . Parent=Match:seg01
|
||||
ctgA example HSP 32329 32359 . + . Parent=Match:seg01
|
||||
@@ -0,0 +1,55 @@
|
||||
##maf version=1
|
||||
a score=60426.0
|
||||
s hg17.chr7 127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
|
||||
s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
|
||||
s mm5.chr6 28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA
|
||||
s rn3.chr4 56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA
|
||||
|
||||
a score=8157.0
|
||||
s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
|
||||
s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
|
||||
s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG
|
||||
|
||||
a score=43613.0
|
||||
s hg17.chr7 127471584 104 + 158628139 GAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt
|
||||
s panTro1.chr6 129885465 104 + 161576975 GAGACATTTGGggaaatt---ttgtatagactagctttcacgatgttagggagttattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt
|
||||
s mm5.chr6 28909125 102 + 149721531 GAGACATTTGGGGGAAATACGATGTATA------CTTTCATGATCTTAAAGAATTGCTATTGTTTGATAGTGATATTATGGTTAAATTAAAAAAAAACCCTTACTTTT
|
||||
s rn3.chr4 56182196 99 + 187371129 GAGATATTTGGGGGAAATATGATGTGCA------CTTCCATGATCTTAAAGAATTGCTACTGTTTGATAGTGATCTTATGGTTAAA-TAAAAAAAAT--CTTAGTTGT
|
||||
s canFam1.chr14 52864846 108 - 63549963 GAGATATTTGGGGGAATTTGAATGTAGTGTTGCTCTTTTGTGATGCTAAGAAATTATAATTGTCTGATGATAGTCTCGTGGTTATGGGGGAAATGCTTCCTTATTTTT
|
||||
|
||||
a score=63217.0
|
||||
s hg17.chr7 127471688 183 + 158628139 tgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaa
|
||||
s panTro1.chr6 129885569 183 + 161576975 tgggaa---acaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacgctttaaaatatttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaaattttcatttaaaaa
|
||||
s mm5.chr6 28909227 176 + 149721531 CATAAA---ATACTCAAATATTTAGGGGTATGACAATGTCATAGTGTCTGCAATTTGCTTTAAAATAATTTTG-------AAAAC---------------------CTGAGGCTAAACTATGGGAA-ATAGCAATTATTACATATGGGTAATAAGTA-----TAACTCACTATATTATTTTTCACTAT----TGTGTTTGAAATTTTCATTTTAAAA
|
||||
s rn3.chr4 56182295 194 + 187371129 TAGAAA---ATACTCAAATATTTAGGGGCGTGACAATGTCACAGTGTCTGCAATTTGCTTTAAAG-ATTTTTAAATATTTAAAAAAGTTTTAATAATTTTGAAAAACTGAAGCTACACTATGGGAA-GTGGTAATTGTTACATATGGGTAATAAGTA-----TAATTCGTTATATTATT-------------TTTCTTAGAATTTTTCATTTGAAAA
|
||||
s canFam1.chr14 52865149 163 - 63549963 tagagacacaaactgaagtatttaaggat---gaaatgtcatgatgtttgcaattggctttaaaatattttag-----ccaaaa-agta----------------aatgaagc--aaatatgggaagacaataatcattaaatctaggtgaTGCATA---------------------------CTTTTCCATATGTTTGAAATTTTCATTTAAAAA
|
||||
|
||||
a score=8913.0
|
||||
s hg17.chr7 127471872 40 + 158628139 ctttgagc-----tagacaccaggctatgagctaggagcatagca
|
||||
s panTro1.chr6 129885753 40 + 161576975 ctttgagc-----tagacaccaggctatgagctaggagcatagca
|
||||
s mm5.chr6 28910662 44 + 149721531 CTTTGTGCTTAGGTAGGCACTGAGCTCTTAAATTGGA-TACAGCG
|
||||
s canFam1.chr14 52865538 40 - 63549963 CATCAtgc-----tagatcctggactatgagctgggtatatagca
|
||||
|
||||
a score=91878.0
|
||||
s hg17.chr7 127471912 335 + 158628139 atgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccggga
|
||||
s panTro1.chr6 129885793 335 + 161576975 atgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaatttttcctg-ggcacccatgtgttcttggcactggaaaagtaccggga
|
||||
s mm5.chr6 28910706 350 + 149721531 ATGAGCAA----------------------------------------------------------------------------------------------AAAAACAACAACAAAAAACAAACAAACAAAAAAACCAAAAACCAAAAACCAAAAAAACCTATAGCCTC-ACAGGGTGGGTTGTCTTTGAGGAACATGCATCCGCTAGAAAGTCCCAAGTACACTATGACAGTTG--CCCAGGCCCCGCCTTAAACCTGGTTTTCCTGGTTTCTTTCA---CATCATTACCACGAATATATTTCCTCAAGTTTAAAGAAAGTACCCCCTCCTTTCCAGT-GCCTCAAATCTAGAAGAATATTCATAGTGAAGT-GCA------------------------CAGCCGGGTGGTGCATGGTAAT-CTGGAAGTCACCTCTGCAAATCTTTCCTG----------------TTGGTGCTGTGAAGGCACCAGGA
|
||||
s rn3.chr4 56183448 420 + 187371129 ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTTGTGCTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC--------------------------------------------------CTC-ACAGGGTGGGTTGTCTTTGAGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGGTTTAAAAGAAGTC-CCACTCCTTTCCAGT-GCCCTAGATCTAGAAGCACATTCATAATGATGT-ACACTAACCCGA---------------CAGCTGTGTGGTATATGGTATC-CCGGAAGTCACCTCAGCAAACCTTTCCCGGGGAACCTACATGGTGTTGGTGCTGTGAAGGTACCAGGT
|
||||
s canFam1.chr14 52865578 336 - 63549963 gtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt--------------------------------------------------cttgatggagcacacaACCTTTGGGGAACATGTTTCCATAAGAAAGTCTCCAATGTGATCTGATGGT-GCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACATTTTAAATATCTG-------CTTCCCGGTGGCCTTGAGTCTAGAGGAGTCCCCCCACTATGGTGGCACTAATACTGAAGGTCAGAAATAATCAGTTCTGTGGTGCATGTTGCCCCTGAGGTTCTGTTCGGGAAACTTCTTCTG-AGCAC----ATGCACCTGGCACTGCAAACGTACCAGGA
|
||||
|
||||
a score=82819.0
|
||||
s hg17.chr7 127472258 423 + 158628139 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgt
|
||||
s panTro1.chr6 129886139 423 + 161576975 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGACCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgtaaatttcctgt
|
||||
s mm5.chr6 28911067 334 + 149721531 AATGGCAGAGGGCTCTGTTCTCT----------------------------------GTCCA---TAGACAAGGAAGC---------CTGCCAGTGG-----------------------TGGAGAGCAGGGCCTATGCAAAACAGGGGGGGTTCTGTGGGCAGAAGGGATGGACCTGACTCCAGGAACGCCCATA-AGAGACGGGCAGGACTGGGAGCCAGGAGCAGCCAGCGCA--------GGTGTGTGTAGGTTTCATAGTTT---------------------------GCAGGTTAGCAAACAATTCTCGCTTGGCAGGCCAAGA-GGGAAAT-AAAGGTTACCCCGTGGGTACTTAT---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTTAATTTCTTAA
|
||||
s rn3.chr4 56183879 340 + 187371129 AATGGCAGAGGCCCCTGTTCTCT----------------------------------GTCCA---TAGTCAAAGAAGC---------CTCTCAG----------------------A---TGGAGAGCAGGGCCTATGCAAAAG-AGGGGGCTTCTGTAGGCAGAAGGGATGGACTAGCCTCCGGACATAGCCATAGAGAGGCTGGCAGGACTGAGACCCAGGAGAAGCCAGCGCAGGTGTGCGGGCGTGTGTATATTTCATAGTTT---------------------------GCAGGTTGGCAAACAATTCCTGCTTTGCAGGCCAAGA-GGAAACT-GAAGGTGACCCCGTGAGTGCTTAC---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTAAATTTCTTTT
|
||||
s canFam1.chr14 52866108 405 - 63549963 GGAGACTTG-ATGCCTGCCTTCCACTTACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAGAAGAGACCCC---------GG--------TGCTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTAACGTG-------CAATGTA------TTTTCTAGTTCCAgggttggcaaactttctctctaagggtgggatgataaacattttaggcttttcagaccaagaggcgacatcagagggtat---gtaggt---------acaagagggaaaagttgcccccggaattttttg--gataaaattcaaaactttacttagggatgccaaaatgtaaacttcatat
|
||||
|
||||
a score=15522.0
|
||||
s hg17.chr7 127473809 97 + 158628139 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgc
|
||||
s panTro1.chr6 129887686 97 + 161576975 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-AAGGCTCGGTTCACCAACATCATTTGC
|
||||
s canFam1.chr14 52866548 97 - 63549963 tatatttttcaactctttaaaaatgcaaaaaccattcctagc-tcggggccatggtggtcctggtggtggtcggatttggctcacccacataacttgc
|
||||
|
||||
a score=28088.0
|
||||
s hg17.chr7 127473906 331 + 158628139 agttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct
|
||||
s panTro1.chr6 129887783 318 + 161576975 AGTTCCCCGCTTTATATTATGGGttttttttttttttttttttttttattgagacagagtttcactcttgttgcccaggctgtagtg--------------tggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcatcatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct
|
||||
|
||||
@@ -204,7 +204,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
self.assertTrue( data_list )
|
||||
if hid is None: # take last hid
|
||||
elem = data_list[-1]
|
||||
hid = elem.get('hid')
|
||||
hid = int( elem.get('hid') )
|
||||
self.assertTrue( hid )
|
||||
self.visit_page( "edit?hid=%d" % hid )
|
||||
for subpatt in patt.split():
|
||||
|
||||
@@ -14,11 +14,11 @@ class UploadData( TwillTestCase ):
|
||||
"""test_get_data.test_multi_upload: Testing multiple uploads"""
|
||||
self.new_history()
|
||||
self.upload_file('1.bed')
|
||||
self.verify_dataset_correctness('1.bed', hid=1)
|
||||
self.verify_dataset_correctness('1.bed')
|
||||
self.upload_file('2.bed', dbkey='hg17')
|
||||
self.verify_dataset_correctness('2.bed', hid=2)
|
||||
self.verify_dataset_correctness('2.bed')
|
||||
self.upload_file('3.bed', dbkey='hg17', ftype='bed')
|
||||
self.verify_dataset_correctness('3.bed', hid=3)
|
||||
self.verify_dataset_correctness('3.bed')
|
||||
|
||||
class GetEncodeData( TwillTestCase ):
|
||||
|
||||
|
||||
@@ -0,0 +1,18 @@
|
||||
from base.twilltestcase import TwillTestCase
|
||||
|
||||
class TestHistory( TwillTestCase ):
|
||||
|
||||
def test_new_history( self ):
|
||||
"""Testing creating a new history"""
|
||||
self.new_history()
|
||||
if len(self.get_datasets_in_history()) > 0:
|
||||
raise AssertionError("test_framework.test_new_history failed")
|
||||
def test_delete_history_item( self ):
|
||||
"""Testing deleting history item"""
|
||||
self.new_history()
|
||||
self.upload_file('1.bed', dbkey='hg15')
|
||||
self.check_history_for_string('hg15 bed')
|
||||
self.assertEqual ( len(self.get_datasets_in_history()), 1)
|
||||
self.delete_history_item(1)
|
||||
self.check_history_for_string("Your history is empty")
|
||||
self.assertEqual ( len(self.get_datasets_in_history()), 0)
|
||||
@@ -1,23 +1,6 @@
|
||||
from base.twilltestcase import TwillTestCase
|
||||
|
||||
class TestHistory( TwillTestCase ):
|
||||
|
||||
def test_new_history( self ):
|
||||
"""test_componments.test_new_history: Testing creating a new history"""
|
||||
self.new_history()
|
||||
if len(self.get_datasets_in_history()) > 0:
|
||||
raise AssertionError("test_framework.test_new_history failed")
|
||||
def test_delete_history_item( self ):
|
||||
"""test_components.test_delete_history_item: Testing deleting history item"""
|
||||
self.new_history()
|
||||
self.upload_file('1.bed', dbkey='hg15')
|
||||
self.check_history_for_string('hg15 bed')
|
||||
self.assertEqual ( len(self.get_datasets_in_history()), 1)
|
||||
self.delete_history_item(1)
|
||||
self.check_history_for_string("Your history is empty")
|
||||
self.assertEqual ( len(self.get_datasets_in_history()), 0)
|
||||
|
||||
class TestMetadata( TwillTestCase ):
|
||||
class TestMetadataEdit( TwillTestCase ):
|
||||
|
||||
def test_metadata_edit(self):
|
||||
"""test_components.test_metadata_edit: Testing metadata editing"""
|
||||
@@ -35,4 +18,3 @@ class TestMetadata( TwillTestCase ):
|
||||
"""test changing data type"""
|
||||
self.edit_metadata(hid=1, form=3, datatype='gff3')
|
||||
self.check_history_for_string('hg16 Testdata Convert BED to GFF format: gff3')
|
||||
|
||||
@@ -0,0 +1,103 @@
|
||||
from base.twilltestcase import TwillTestCase
|
||||
|
||||
class SniffingAndMetaDataSettings( TwillTestCase ):
|
||||
|
||||
def test_axt_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing axt data type upon upload"""
|
||||
self.upload_file('1.axt')
|
||||
self.verify_dataset_correctness('1.axt')
|
||||
self.check_history_for_string('1.axt format: <span class="axt">axt</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="1.axt" value="\?" Change data type selected value="axt" selected="yes"')
|
||||
def test_bed_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing bed data type upon upload"""
|
||||
self.upload_file('1.bed')
|
||||
self.verify_dataset_correctness('1.bed')
|
||||
self.check_history_for_string('1.bed format: <span class="bed">bed</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="1.bed" value="\?"')
|
||||
self.check_metadata_for_string('Chrom column: <option value="1" selected> Start column: <option value="2" selected>')
|
||||
self.check_metadata_for_string('End column: <option value="3" selected> Strand column <option value="6" selected>')
|
||||
self.check_metadata_for_string('Convert to new format <option value="bed">Genomic Intervals To BED <option value="gff">BED to GFF')
|
||||
self.check_metadata_for_string('Change data type selected value="bed" selected="yes"')
|
||||
def test_customtrack_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing customtrack data type upon upload"""
|
||||
self.upload_file('1.customtrack')
|
||||
self.verify_dataset_correctness('1.customtrack')
|
||||
self.check_history_for_string('1.customtrack format: <span class="customtrack">customtrack</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="1.customtrack" value="\?" Change data type selected value="customtrack" selected="yes"')
|
||||
def test_fasta_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing fasta data type upon upload"""
|
||||
self.upload_file('1.fasta')
|
||||
self.verify_dataset_correctness('1.fasta')
|
||||
self.check_history_for_string('1.fasta format: <span class="fasta">fasta</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="1.fasta" value="\?" Change data type selected value="fasta" selected="yes"')
|
||||
def test_gff_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing gff data type upon upload"""
|
||||
self.upload_file('5.gff')
|
||||
self.verify_dataset_correctness('5.gff')
|
||||
self.check_history_for_string('5.gff format: <span class="gff">gff</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="5.gff" value="\?"')
|
||||
self.check_metadata_for_string('Convert to new format <option value="bed">GFF to BED')
|
||||
self.check_metadata_for_string('Change data type selected value="gff" selected="yes"')
|
||||
def test_gff3_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing gff3 data type upon upload"""
|
||||
self.upload_file('5.gff3')
|
||||
self.verify_dataset_correctness('5.gff3')
|
||||
self.check_history_for_string('5.gff3 format: <span class="gff3">gff3</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="5.gff3" value="\?"')
|
||||
self.check_metadata_for_string('Convert to new format <option value="bed">GFF to BED')
|
||||
self.check_metadata_for_string('Change data type selected value="gff3" selected="yes"')
|
||||
def test_html_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing html data type upon upload"""
|
||||
self.upload_file('html_file.txt')
|
||||
self.check_history_for_string('No data: attempted to upload an empty or inappropriate file')
|
||||
def test_interval_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing interval data type upon upload"""
|
||||
self.upload_file('1.interval')
|
||||
self.verify_dataset_correctness('1.interval')
|
||||
self.check_history_for_string('1.interval format: <span class="interval">interval</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="1.interval" value="\?"')
|
||||
self.check_metadata_for_string('Chrom column: <option value="1" selected> Start column: <option value="2" selected>')
|
||||
self.check_metadata_for_string('End column: <option value="3" selected> Strand column <option value="6" selected>')
|
||||
self.check_metadata_for_string('Convert to new format <option value="bed">Genomic Intervals To BED')
|
||||
self.check_metadata_for_string('Change data type selected value="interval" selected="yes"')
|
||||
def test_lav_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing lav data type upon upload"""
|
||||
self.upload_file('1.lav')
|
||||
self.verify_dataset_correctness('1.lav')
|
||||
self.check_history_for_string('1.lav format: <span class="lav">lav</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="1.lav" value="\?"')
|
||||
self.check_metadata_for_string('Change data type selected value="lav" selected="yes"')
|
||||
def test_maf_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing maf data type upon upload"""
|
||||
self.upload_file('3.maf')
|
||||
self.verify_dataset_correctness('3.maf')
|
||||
self.check_history_for_string('3.maf format: <span class="maf">maf</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="3.maf" value="\?"')
|
||||
self.check_metadata_for_string('Convert to new format <option value="interval">MAF to Genomic Intervals <option value="fasta">MAF to Fasta')
|
||||
self.check_metadata_for_string('Change data type selected value="maf" selected="yes"')
|
||||
def test_tabular_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing tabular data type upon upload"""
|
||||
self.upload_file('1.tabular')
|
||||
self.verify_dataset_correctness('1.tabular')
|
||||
self.check_history_for_string('1.tabular format: <span class="tabular">tabular</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="1.tabular" value="\?"')
|
||||
self.check_metadata_for_string('Change data type selected value="tabular" selected="yes"')
|
||||
def test_wig_datatype( self ):
|
||||
self.new_history()
|
||||
"""Testing correctly sniffing wig data type upon upload"""
|
||||
self.upload_file('1.wig')
|
||||
self.verify_dataset_correctness('1.wig')
|
||||
self.check_history_for_string('1.wig format: <span class="wig">wig</span>, database: \? Info: uploaded file')
|
||||
self.check_metadata_for_string('value="1.wig" value="\?"')
|
||||
self.check_metadata_for_string('Change data type selected value="wig" selected="yes"')
|
||||
@@ -16,7 +16,7 @@
|
||||
<param name="input1" value="3.maf" ftype="maf" />
|
||||
<param name="min_size" value="0"/>
|
||||
<param name="max_size" value="0"/>
|
||||
<output name="out_file1" file="3.maf" />
|
||||
<output name="out_file1" file="maf_limit_size1_out.maf" />
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
|
||||
Reference in New Issue
Block a user