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Corrected typo in tool name and enhanced error messages.

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This commit is contained in:
Guruprasad Anada
2007-05-30 17:33:20 +00:00
parent be673c2a5a
commit 7ab8bb1450
2 changed files with 12 additions and 9 deletions
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tools/extract/twoBitToFa_wrapper.py
+11 -8
View File
@@ -15,7 +15,7 @@ def reverse_complement(text):
return "".join(comp)
if len(sys.argv) != 9:
print "USAGE: prog input out_file input_chromCol input_startCol input_endCol input_strandCol input_dbkey loc_file"
print >>sys.stderr, "USAGE: prog input out_file input_chromCol input_startCol input_endCol input_strandCol input_dbkey loc_file"
sys.exit()
infile = sys.argv[1]
@@ -52,7 +52,8 @@ except Exception, exc:
print >>sys.stdout, 'twoBitToFa_wrapper.py initialization error -> %s' % exc
if filepath == None:
print "Sequences for the specified genome are unavailable. You may want to try the 'Extract genomic DNA corresponding to query coordinates' tool"
print >>sys.stderr, "Sequences for the specified genome are unavailable. You may want to try the 'Extract genomic DNA corresponding to query coordinates' tool"
sys.exit()
else:
try:
fout = open(outfile, "w")
@@ -66,27 +67,29 @@ else:
end = fields[int(end_col)-1]
#Run twoBitToFa program
tmpfile = tempfile.NamedTemporaryFile()
cmdline = "tools/extract/twoBitToFa " + filepath.strip() + " " + tmpfile.name + " -seq=" + name + " -start=" + start + " -end=" + end
cmdline = "tools/extract/twoBitToFa " + filepath.strip() + " " + tmpfile.name + " -seq=" + name + " -start=" + start + " -end=" + end + " > /dev/null 2>&1"
os.system(cmdline)
header = tmpfile.readline()
seq = tmpfile.read()
if header == "" and seq == "":
print >>sys.stderr, '%s:%s-%s is either invalid or not present in the specified genome.' %(name,start,end)
continue
if strand_col != 0 and fields[int(strand_col)-1] == "-": # for negative strand
print >>fout, header.strip()
revcompseq = reverse_complement(seq.replace("\n","").replace("\r",""))
i = 0
while i < len (revcompseq):
print >>fout, revcompseq[i:i+50] #print 50 nucleotides per line of the fasta output
print >>fout, revcompseq[i:i+50].strip() #print 50 nucleotides per line of the fasta output
i += 50
#print >>fout, reverse_complement(seq.replace("\n","").replace("\r",""))
else: # for positive strand
print >>fout, header.strip()
print >>fout, seq
print >>fout, seq.strip()
except:
pass #skip invalid lines
fout.close()
print "Genomic DNA corresponding to query co-ordinates"
print "Genomic DNA corresponding to query co-ordinates:"
except Exception, exc:
print >>sys.stdout, exc
print >>sys.stderr, exc
tools/extract/twoBitToFa_wrapper.xml
+1 -1
View File
@@ -1,4 +1,4 @@
<tool id="Extract genomic DNA" name="Extract genomic DNA2">
<tool id="Extract genomic DNA2" name="Extract genomic DNA">
<description>from unassembled genome coordinates</description>
<command interpreter="perl">twoBitToFa_wrapper.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey "/depot/data2/galaxy/twobit.loc"</command>
<inputs>