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Minor update to interval2maf.py display of error messages.

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This commit is contained in:
Daniel Blankenberg
2007-11-16 17:39:49 +00:00
parent 538db8bd09
commit 0e9c5bdbd9
1 changed files with 57 additions and 58 deletions
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tools/extract/interval2maf.py
+57 -58
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@@ -70,75 +70,74 @@ def build_maf_index( maf_file, species = None ):
return ( None, None )
def __main__():
# Parse Command Line
options, args = doc_optparse.parse( __doc__ )
index = index_filename = None
mincols = 0
try:
if options.dbkey: dbkey = options.dbkey
else: dbkey = None
if dbkey in [None, "?"]:
print >>sys.stderr, "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file."
# Parse Command Line
options, args = doc_optparse.parse( __doc__ )
if options.dbkey: dbkey = options.dbkey
else: dbkey = None
if dbkey in [None, "?"]:
print >>sys.stderr, "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file."
sys.exit()
species = None
if options.species:
species = options.species.split( ',' )
if "None" in species: species = None
if options.chromCol: chromCol = int( options.chromCol ) - 1
else:
print >>sys.stderr, "Chromosome column has not been specified."
sys.exit()
if options.startCol: startCol = int( options.startCol ) - 1
else:
print >>sys.stderr, "Start column has not been specified."
sys.exit()
if options.endCol: endCol = int( options.endCol ) - 1
else:
print >>sys.stderr, "End column has not been specified."
sys.exit()
if options.strandCol: strandCol = int( options.strandCol ) - 1
else:
print >>sys.stderr, "Strand column has not been specified."
sys.exit()
if options.interval_file: interval_file = options.interval_file
else:
print >>sys.stderr, "Input interval file has not been specified."
sys.exit()
if options.output_file: output_file = options.output_file
else:
print >>sys.stderr, "Output file has not been specified."
sys.exit()
#Open indexed access to MAFs
if options.mafType:
index = maf_index_by_uid( options.mafType )
if index is None:
print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( options.mafType )
sys.exit()
if options.species: species = options.species.split( ',' )
else: species = None
if options.chromCol: chromCol= int(options.chromCol) - 1
else:
print >>sys.stderr, "Chromosome column has not been specified."
elif options.mafFile:
index, index_filename = build_maf_index( options.mafFile, species = [dbkey] )
if index is None:
print >> sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
if options.startCol: startCol= int(options.startCol) - 1
else:
print >>sys.stderr, "Start column has not been specified."
sys.exit()
if options.endCol: endCol= int(options.endCol) - 1
else:
print >>sys.stderr, "End column has not been specified."
sys.exit()
if options.strandCol: strandCol= int(options.strandCol) - 1
else:
print >>sys.stderr, "Strand column has not been specified."
sys.exit()
if options.interval_file: interval_file= options.interval_file
else:
print >>sys.stderr, "Input interval file has not been specified."
sys.exit()
if options.output_file: output_file= options.output_file
else:
print >>sys.stderr, "Output file has not been specified."
sys.exit()
#Open indexed access to MAFs
if options.mafType:
index = maf_index_by_uid( options.mafType )
if index is None:
print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( options.mafType )
sys.exit()
elif options.mafFile:
index, index_filename = build_maf_index( options.mafFile, species = [dbkey] )
if index is None:
print >> sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
else:
print >>sys.stderr, "Desired source MAF type has not been specified."
sys.exit()
except Exception, exc:
print >>sys.stdout, 'interval2maf.py initialization error -> %s' % exc
else:
print >>sys.stderr, "Desired source MAF type has not been specified."
sys.exit()
out = bx.align.maf.Writer( open(output_file, "w") )
# Iterate over input regions
num_blocks = 0
num_lines = 0
for num_lines, region in enumerate( bx.intervals.io.NiceReaderWrapper( open(interval_file, 'r' ), chrom_col = chromCol, start_col = startCol, end_col = endCol, strand_col = strandCol, fix_strand = True, return_header = False, return_comments = False ) ):
for num_lines, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( interval_file, 'r' ), chrom_col = chromCol, start_col = startCol, end_col = endCol, strand_col = strandCol, fix_strand = True, return_header = False, return_comments = False ) ):
try:
src = "%s.%s" % ( dbkey, region.chrom )