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Better error handling in extract_genomic_dna tool, behavior doesn't change so new version not necessary.

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This commit is contained in:
Greg Von Kuster
2008-02-05 20:13:07 +00:00
parent e15b218725
commit 2e032d917f
1 changed files with 11 additions and 9 deletions
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tools/extract/extract_genomic_dna.py
+11 -9
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@@ -99,6 +99,7 @@ def __main__():
first_invalid_line = 0
invalid_line = ''
fout = open( output_filename, "w" )
err_msg = ''
for i, line in enumerate( open( input_filename ) ):
line = line.rstrip( '\r\n' )
@@ -122,8 +123,8 @@ def __main__():
try:
sequence = nib.get( start, end-start )
except:
fout.close()
stop_err( "Unable to fetch the sequence from %d to %d from %s." %( start, end-start, nib_path ) )
err_msg = "Unable to fetch the sequence from %d to %d from %s." %( start, end-start, nib_path )
break
elif os.path.exists( twobit_path ):
if chrom in twobits:
t = twobits[chrom]
@@ -132,15 +133,15 @@ def __main__():
try:
sequence = t[chrom][start:end]
except:
fout.close()
stop_err( "Unable to fetch the sequence from %d to %d from %s." %( start, end-start, twobit_path ) )
err_msg = "Unable to fetch the sequence from %d to %d from %s." %( start, end-start, twobit_path )
break
else:
fout.close()
stop_err( "Sequence %s was not found for build %s. Most likely your data lists the wrong chromosome number for this organism. Check your build selection." % ( chrom, dbkey ) )
err_msg = "Sequence %s was not found for build %s. Most likely your data lists the wrong chromosome number for this organism. Check your build selection." % ( chrom, dbkey )
break
if not sequence:
fout.close()
stop_err( '%s_%s_%s is either invalid or not present in the specified build.' %( chrom, start, end ) )
err_msg = "%s_%s_%s is either invalid or not present in the specified build." %( chrom, start, end )
break
if includes_strand_col and strand == "-":
sequence = reverse_complement( sequence )
@@ -163,7 +164,8 @@ def __main__():
first_invalid_line = i + 1
invalid_line = line
fout.close()
if err_msg:
stop_err( err_msg )
if skipped_lines:
print 'Data issue: skipped %d invalid lines starting at line #%d, "%s"' % ( skipped_lines, first_invalid_line, invalid_line )