/usr/share/pyshared/HTSeq/scripts/count.py is in python-htseq 0.5.4p3-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import HTSeq
class UnknownChrom( Exception ):
pass
def invert_strand( iv ):
iv2 = iv.copy()
if iv2.strand == "+":
iv2.strand = "-"
elif iv2.strand == "-":
iv2.strand = "+"
else:
raise ValueError, "Illegal strand"
return iv2
def count_reads_in_features( sam_filename, gff_filename, stranded,
overlap_mode, feature_type, id_attribute, quiet, minaqual, samout ):
def write_to_samout( r, assignment ):
if samoutfile is None:
return
if not pe_mode:
r = (r,)
for read in r:
if read is not None:
samoutfile.write( read.original_sam_line.rstrip() +
"\tXF:Z:" + assignment + "\n" )
if quiet:
warnings.filterwarnings( action="ignore", module="HTSeq" )
if samout != "":
samoutfile = open( samout, "w" )
else:
samoutfile = None
features = HTSeq.GenomicArrayOfSets( "auto", stranded != "no" )
counts = {}
# Try to open samfile to fail early in case it is not there
if sam_filename != "-":
open( sam_filename ).close()
gff = HTSeq.GFF_Reader( gff_filename )
i = 0
try:
for f in gff:
if f.type == feature_type:
try:
feature_id = f.attr[ id_attribute ]
except KeyError:
sys.exit( "Feature %s does not contain a '%s' attribute" %
( f.name, id_attribute ) )
if stranded != "no" and f.iv.strand == ".":
sys.exit( "Feature %s at %s does not have strand information but you are "
"running htseq-count in stranded mode. Use '--stranded=no'." %
( f.name, f.iv ) )
features[ f.iv ] += feature_id
counts[ f.attr[ id_attribute ] ] = 0
i += 1
if i % 100000 == 0 and not quiet:
sys.stderr.write( "%d GFF lines processed.\n" % i )
except:
sys.stderr.write( "Error occured in %s.\n" % gff.get_line_number_string() )
raise
if not quiet:
sys.stderr.write( "%d GFF lines processed.\n" % i )
if len( counts ) == 0 and not quiet:
sys.stderr.write( "Warning: No features of type '%s' found.\n" % feature_type )
try:
if sam_filename != "-":
read_seq = HTSeq.SAM_Reader( sam_filename )
first_read = iter(read_seq).next()
else:
read_seq = iter( HTSeq.SAM_Reader( sys.stdin ) )
first_read = read_seq.next()
read_seq = itertools.chain( [ first_read ], read_seq )
pe_mode = first_read.paired_end
except:
sys.stderr.write( "Error occured when reading first line of sam file.\n" )
raise
try:
if pe_mode:
read_seq_pe_file = read_seq
read_seq = HTSeq.pair_SAM_alignments( read_seq )
empty = 0
ambiguous = 0
notaligned = 0
lowqual = 0
nonunique = 0
i = 0
for r in read_seq:
i += 1
if not pe_mode:
if not r.aligned:
notaligned += 1
write_to_samout( r, "not_aligned" )
continue
try:
if r.optional_field( "NH" ) > 1:
write_to_samout( r, "alignment_not_unique" )
nonunique += 1
continue
except KeyError:
pass
if r.aQual < minaqual:
lowqual += 1
write_to_samout( r, "too_low_aQual" )
continue
if stranded != "reverse":
iv_seq = ( co.ref_iv for co in r.cigar if co.type == "M" and co.size > 0 )
else:
iv_seq = ( invert_strand( co.ref_iv ) for co in r.cigar if co.type == "M" and co.size > 0 )
else:
if r[0] is not None and r[0].aligned:
if stranded != "reverse":
iv_seq = ( co.ref_iv for co in r[0].cigar if co.type == "M" and co.size > 0 )
else:
iv_seq = ( invert_strand( co.ref_iv ) for co in r[0].cigar if co.type == "M" and co.size > 0 )
else:
iv_seq = tuple()
if r[1] is not None and r[1].aligned:
if stranded != "reverse":
iv_seq = itertools.chain( iv_seq,
( invert_strand( co.ref_iv ) for co in r[1].cigar if co.type == "M" and co.size > 0 ) )
else:
iv_seq = itertools.chain( iv_seq,
( co.ref_iv for co in r[1].cigar if co.type == "M" and co.size > 0 ) )
else:
if ( r[0] is None ) or not ( r[0].aligned ):
write_to_samout( r, "not_aligned" )
notaligned += 1
continue
try:
if ( r[0] is not None and r[0].optional_field( "NH" ) > 1 ) or \
( r[1] is not None and r[1].optional_field( "NH" ) > 1 ):
nonunique += 1
write_to_samout( r, "alignment_not_unique" )
continue
except KeyError:
pass
if ( r[0] and r[0].aQual < minaqual ) or ( r[1] and r[1].aQual < minaqual ):
lowqual += 1
write_to_samout( r, "too_low_aQual" )
continue
try:
if overlap_mode == "union":
fs = set()
for iv in iv_seq:
if iv.chrom not in features.chrom_vectors:
raise UnknownChrom
for iv2, fs2 in features[ iv ].steps():
fs = fs.union( fs2 )
elif overlap_mode == "intersection-strict" or overlap_mode == "intersection-nonempty":
fs = None
for iv in iv_seq:
if iv.chrom not in features.chrom_vectors:
raise UnknownChrom
for iv2, fs2 in features[ iv ].steps():
if len(fs2) > 0 or overlap_mode == "intersection-strict":
if fs is None:
fs = fs2.copy()
else:
fs = fs.intersection( fs2 )
else:
sys.exit( "Illegal overlap mode." )
if fs is None or len( fs ) == 0:
write_to_samout( r, "no_feature" )
empty += 1
elif len( fs ) > 1:
write_to_samout( r, "ambiguous[" + '+'.join( fs ) + "]" )
ambiguous += 1
else:
write_to_samout( r, list(fs)[0] )
counts[ list(fs)[0] ] += 1
except UnknownChrom:
if not pe_mode:
rr = r
else:
rr = r[0] if r[0] is not None else r[1]
empty += 1
#if not quiet:
# sys.stderr.write( ( "Warning: Skipping read '%s', because chromosome " +
# "'%s', to which it has been aligned, did not appear in the GFF file.\n" ) %
# ( rr.read.name, iv.chrom ) )
if i % 100000 == 0 and not quiet:
sys.stderr.write( "%d sam %s processed.\n" % ( i, "lines " if not pe_mode else "line pairs" ) )
except:
if not pe_mode:
sys.stderr.write( "Error occured in %s.\n" % read_seq.get_line_number_string() )
else:
sys.stderr.write( "Error occured in %s.\n" % read_seq_pe_file.get_line_number_string() )
raise
if not quiet:
sys.stderr.write( "%d sam %s processed.\n" % ( i, "lines " if not pe_mode else "line pairs" ) )
if samoutfile is not None:
samoutfile.close()
for fn in sorted( counts.keys() ):
print "%s\t%d" % ( fn, counts[fn] )
print "no_feature\t%d" % empty
print "ambiguous\t%d" % ambiguous
print "too_low_aQual\t%d" % lowqual
print "not_aligned\t%d" % notaligned
print "alignment_not_unique\t%d" % nonunique
def main():
optParser = optparse.OptionParser(
usage = "%prog [options] sam_file gff_file",
description=
"This script takes an alignment file in SAM format and a " +
"feature file in GFF format and calculates for each feature " +
"the number of reads mapping to it. See " +
"http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.",
epilog =
"Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology " +
"Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General " +
"Public License v3. Part of the 'HTSeq' framework, version %s." % HTSeq.__version__ )
optParser.add_option( "-m", "--mode", type="choice", dest="mode",
choices = ( "union", "intersection-strict", "intersection-nonempty" ),
default = "union", help = "mode to handle reads overlapping more than one feature" +
"(choices: union, intersection-strict, intersection-nonempty; default: union)" )
optParser.add_option( "-s", "--stranded", type="choice", dest="stranded",
choices = ( "yes", "no", "reverse" ), default = "yes",
help = "whether the data is from a strand-specific assay. Specify 'yes', " +
"'no', or 'reverse' (default: yes). " +
"'reverse' means 'yes' with reversed strand interpretation" )
optParser.add_option( "-a", "--minaqual", type="int", dest="minaqual",
default = 0,
help = "skip all reads with alignment quality lower than the given " +
"minimum value (default: 0)" )
optParser.add_option( "-t", "--type", type="string", dest="featuretype",
default = "exon", help = "feature type (3rd column in GFF file) to be used, " +
"all features of other type are ignored (default, suitable for Ensembl " +
"GTF files: exon)" )
optParser.add_option( "-i", "--idattr", type="string", dest="idattr",
default = "gene_id", help = "GFF attribute to be used as feature ID (default, " +
"suitable for Ensembl GTF files: gene_id)" )
optParser.add_option( "-o", "--samout", type="string", dest="samout",
default = "", help = "write out all SAM alignment records into an output " +
"SAM file called SAMOUT, annotating each line with its feature assignment " +
"(as an optional field with tag 'XF')" )
optParser.add_option( "-q", "--quiet", action="store_true", dest="quiet",
help = "suppress progress report and warnings" )
if len( sys.argv ) == 1:
optParser.print_help()
sys.exit(1)
(opts, args) = optParser.parse_args()
if len( args ) != 2:
sys.stderr.write( sys.argv[0] + ": Error: Please provide two arguments.\n" )
sys.stderr.write( " Call with '-h' to get usage information.\n" )
sys.exit( 1 )
warnings.showwarning = my_showwarning
try:
count_reads_in_features( args[0], args[1], opts.stranded,
opts.mode, opts.featuretype, opts.idattr, opts.quiet, opts.minaqual,
opts.samout )
except:
sys.stderr.write( "Error: %s\n" % str( sys.exc_info()[1] ) )
sys.stderr.write( "[Exception type: %s, raised in %s:%d]\n" %
( sys.exc_info()[1].__class__.__name__,
os.path.basename(traceback.extract_tb( sys.exc_info()[2] )[-1][0]),
traceback.extract_tb( sys.exc_info()[2] )[-1][1] ) )
sys.exit( 1 )
def my_showwarning( message, category, filename, lineno = None, line = None ):
sys.stderr.write( "Warning: %s\n" % message )
if __name__ == "__main__":
main()
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