opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-21 13:50:20 +08:00
Code Issues Packages Projects Releases Wiki Activity

More changes to mutability tool.

Browse Source
This commit is contained in:
Guruprasad Anada
2009-01-15 13:10:04 -05:00
parent b7aaa17bc3
commit ee8779987e
2 changed files with 16 additions and 17 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/regVariation/microsats_mutability.py
+12 -17
View File
@@ -128,11 +128,13 @@ def output_writer(blk, blk_lines):
uniq_s_elems_2 = get_binned_lists(uniq_s_elems_2,s_bin_size)
for pitem1 in uniq_elems_1:
repeats1 = []
repeats2 = []
#repeats1 = []
#repeats2 = []
thresholds = []
if s_group_cols[0] != -1: #Sub-group by feature is not None
for sitem1 in uniq_s_elems_1:
repeats1 = []
repeats2 = []
if type(sitem1) == type(''):
sitem1 = sitem1.strip()
for bline in blk_lines:
@@ -223,11 +225,13 @@ def output_writer(blk, blk_lines):
count1[str(pitem1)]=sum(repeats2)
for pitem2 in uniq_elems_2:
repeats1 = []
repeats2 = []
#repeats1 = []
#repeats2 = []
thresholds = []
if s_group_cols[0] != -1: #Sub-group by feature is not None
for sitem2 in uniq_s_elems_2:
repeats1 = []
repeats2 = []
if type(sitem2)==type(''):
sitem2 = sitem2.strip()
for bline in blk_lines:
@@ -349,11 +353,10 @@ def output_writer(blk, blk_lines):
count = count1[key]
mut = "%.2e" %(mut/num_generations)
if region == 'align':
print >>fout, str(blk) + '\t'+seq1 + '\t' + start1+ '\t'+end1+ '\t'+seq2 + '\t'+start2+ '\t'+end2+ '\t'+key.strip()+ '\t'+str(mut) + '\t'+ str(count)
print >>fout, str(blk) + '\t'+seq1 + '\t' + seq2 + '\t' +key.strip()+ '\t'+str(mut) + '\t'+ str(count)
elif region == 'win':
fout.write("%s\t%s\t%s\t%s\n" %(blk,key.strip(),mut,count))
fout.flush()
#print >>fout, blk + '\t'+key.strip()+ '\t'+str(mut)+ '\t'+ str(count)
#catch any remaining repeats, for instance if the orthologous position contained different repeat units
for remaining_key in mut2.keys():
@@ -361,7 +364,7 @@ def output_writer(blk, blk_lines):
mut = "%.2e" %(mut/num_generations)
count = count2[remaining_key]
if region == 'align':
print >>fout, str(blk) + '\t'+seq1 + '\t' + start1+ '\t'+end1+ '\t'+seq2 + '\t'+start2+ '\t'+end2+ '\t'+remaining_key.strip()+ '\t'+str(mut)+ '\t'+ str(count)
print >>fout, str(blk) + '\t'+seq1 + '\t'+seq2 + '\t'+remaining_key.strip()+ '\t'+str(mut)+ '\t'+ str(count)
elif region == 'win':
fout.write("%s\t%s\t%s\t%s\n" %(blk,remaining_key.strip(),mut,count))
fout.flush()
@@ -420,17 +423,9 @@ def main():
fix_strand = True)
msatTree = quicksect.IntervalTree()
for item in msats:
#print >>sys.stderr, item
if type( item ) is GenomicInterval:
msatTree.insert( item, msats.linenum, item.fields )
"""
result = []
msatTree.traverse(lambda node: result.append( node ))
for n in result:
print >>sys.stderr,n.other
print >>sys.stderr,msatTree.chroms
#sys.exit()
"""
for iline in fint:
try:
iline = iline.rstrip('\r\n')
@@ -460,7 +455,7 @@ def main():
print "Skipped %d intervals as invalid." %(skipped)
elif region == 'align':
if s_group_cols[0] != -1:
print >>fout, "#Window\tSpecies_1\tWindow_Start\tWindow_End\tSpecies_2\tGroupby_Feature\tSubGroupby_Feature\tMutability\tCount"
print >>fout, "#Window\tSpecies_1\tSpecies_2\tGroupby_Feature\tSubGroupby_Feature\tMutability\tCount"
else:
print >>fout, "#Window\tSpecies_1\tWindow_Start\tWindow_End\tSpecies_2\tGroupby_Feature\tMutability\tCount"
prev_bnum = -1
tools/regVariation/microsats_mutability.xml
+4
View File
@@ -106,6 +106,10 @@
This tool computes microsatellite mutability for the orthologous microsatellites fetched from 'Extract Orthologous Microsatellites from pair-wise alignments' tool.
Mutability is computed according to the method described in the following paper:
*Webster et al., Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments, Proc Natl Acad Sci 2002 June 25; 99(13): 8748-8753*
-----
.. class:: warningmark