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More tool code cleanup, more informative messages, forgot to reset tool id in extract genomic dna tool.

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This commit is contained in:
Greg Von Kuster
2008-03-10 17:40:31 +00:00
parent d719431ad3
commit 34ba38d50a
3 changed files with 10 additions and 24 deletions
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tools/encode/split_by_partitions.py
+1 -1
View File
@@ -112,7 +112,7 @@ def main():
in_file.close()
if warnings:
warn_msg = "Total of %d warnings, 1st is: " % len( warnings )
warn_msg = "This tool is useful on ENCODE regions only, %d warnings, 1st is: " % len( warnings )
warn_msg += warnings[0]
print warn_msg
if skipped_lines:
tools/extract/extract_genomic_dna.xml
+2 -2
View File
@@ -1,4 +1,4 @@
<tool id="Extract_genomic_DNA_1" name="Extract Genomic DNA" version="2.0.0">
<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.0.0">
<description>using coordinates from assembled/unassebmled genomes</description>
<command interpreter="python">extract_genomic_dna.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey $out_format</command>
<inputs>
@@ -35,7 +35,7 @@
.. class:: warningmark
This tool requires tabular formatted data!
This tool requires tabular formatted data. If your data is not TAB delimited, use *Edit Queries-&gt;Convert characters*.
.. class:: warningmark
tools/new_operations/flanking_features.py
+7 -21
View File
@@ -20,7 +20,6 @@ def stop_err( msg ):
def main():
infile1_includes_strand = False
# Parsing Command Line here
options, args = doc_optparse.parse( __doc__ )
try:
@@ -81,10 +80,12 @@ def main():
if line and not line.startswith( '#' ):
try:
elems = line.split( '\t' )
#if the start and/or end columns are not numbers, skip that line.
chr = elems[chr_col_1]
start = int( elems[start_col_1] )
end = int( elems[end_col_1] )
if infile1_includes_strand:
strand = elems[strand_col_1]
assert strand in ['+', '-']
except:
skipped_lines += 1
if not invalid_line:
@@ -92,27 +93,13 @@ def main():
invalid_line = line
continue
if infile1_includes_strand:
#Strand column is defined
try:
strand = elems[strand_col_1]
#if the stand value is not + or -, skip that line.
assert strand in ['+', '-']
except:
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if direction == 'Upstream' or direction == 'Both':
for fline in file( tmp_file_up ):
fline = fline.rstrip( '\r\n' )
if fline and not fline.startswith( '#' ):
try:
felems = fline.split( '\t' )
fchr = felems[chr_col_2]
if fchr != chr:
if chr != felems[chr_col_2]:
continue
if infile1_includes_strand:
try:
@@ -125,11 +112,11 @@ def main():
continue
fstart = int( felems[start_col_2] )
fend = int( felems[end_col_2] )
if strand == '+'and fend < start:
if strand == '+' and fend < start:
#Highest feature end value encountered i.e. the closest upstream feature found
fo.write( "%s\t%s\n" % ( line, fline ) )
break
elif strand == '-'and fstart > end:
elif strand == '-' and fstart > end:
#Lowest feature start value encountered i.e. the closest upstream feature found
fo.write( "%s\t%s\n" % ( line, fline ) )
break
@@ -141,8 +128,7 @@ def main():
if fline and not fline.startswith( '#' ):
try:
felems = fline.split( '\t' )
fchr = felems[chr_col_2]
if fchr != chr:
if chr != felems[chr_col_2]:
continue
if infile1_includes_strand:
try: