def main():
skipped = 0
not_pairwise = 0
if int_file == "None":
try:
maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
except:
stop_err("Your MAF file appears to be malformed.")
print >>fout, "#Seq1\tStart1\tEnd1\tSeq2\tStart2\tEnd2\tL\tN\tp"
for block in maf_reader:
if len(block.components) != 2:
not_pairwise += 1
continue
try:
rateEstimator(block)
except:
skipped += 1
else:
index, index_filename = maf_utilities.build_maf_index( inp_file, species = [dbkey_i] )
if index is None:
print >> sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
win = NiceReaderWrapper( fileinput.FileInput( int_file ),
chrom_col=chr_col_i,
start_col=start_col_i,
end_col=end_col_i,
strand_col=strand_col_i,
fix_strand=True)
species=None
mincols = 0
global alignlen, mismatches
for interval in win:
alignlen = 0
mismatches = 0.0
src = "%s.%s" % ( dbkey_i, interval.chrom )
for block in maf_utilities.get_chopped_blocks_for_region( index, src, interval, species, mincols ):
if len(block.components) != 2:
not_pairwise += 1
continue
try:
rateEstimator(block)
except:
skipped += 1
if alignlen:
p = mismatches/alignlen
else:
p = 'NA'
interval.fields.append(str(alignlen))
interval.fields.append(str(mismatches))
interval.fields.append(str(p))
print >>fout, "\t".join(interval.fields)
#num_blocks += 1
if not_pairwise:
print "Skipped %d non-pairwise blocks" %(not_pairwise)
if skipped:
print "Skipped %d blocks as invalid" %(skipped)
def main():
skipped = 0
not_pairwise = 0
if int_file == "None":
try:
maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
except:
stop_err("Your MAF file appears to be malformed.")
print >> fout, "#Seq1\tStart1\tEnd1\tSeq2\tStart2\tEnd2\tL\tN\tp"
for block in maf_reader:
if len(block.components) != 2:
not_pairwise += 1
continue
try:
rateEstimator(block)
except:
skipped += 1
else:
index, index_filename = maf_utilities.build_maf_index( inp_file, species = [dbkey_i] )
if index is None:
print >> sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
win = NiceReaderWrapper( fileinput.FileInput( int_file ),
chrom_col=chr_col_i,
start_col=start_col_i,
end_col=end_col_i,
strand_col=strand_col_i,
fix_strand=True)
species = None
mincols = 0
global alignlen, mismatches
for interval in win:
alignlen = 0
mismatches = 0.0
src = "%s.%s" % ( dbkey_i, interval.chrom )
for block in maf_utilities.get_chopped_blocks_for_region( index, src, interval, species, mincols ):
if len(block.components) != 2:
not_pairwise += 1
continue
try:
rateEstimator(block)
except:
skipped += 1
if alignlen:
p = mismatches/alignlen
else:
p = 'NA'
interval.fields.append(str(alignlen))
interval.fields.append(str(mismatches))
interval.fields.append(str(p))
print >> fout, "\t".join(interval.fields)
#num_blocks += 1
if not_pairwise:
print "Skipped %d non-pairwise blocks" % (not_pairwise)
if skipped:
print "Skipped %d blocks as invalid" % (skipped)
def __main__():
maf_source_type = sys.argv.pop( 1 )
input_maf_filename = sys.argv[1].strip()
input_interval_filename = sys.argv[2].strip()
output_filename = sys.argv[3].strip()
dbkey = sys.argv[4].strip()
try:
chr_col = int( sys.argv[5].strip() ) - 1
start_col = int( sys.argv[6].strip() ) - 1
end_col = int( sys.argv[7].strip() ) - 1
except:
print >>sys.stderr, "You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file."
sys.exit()
summary = sys.argv[8].strip()
if summary.lower() == "true": summary = True
else: summary = False
mafIndexFile = "%s/maf_index.loc" % sys.argv[9]
try:
maf_index_filename = sys.argv[10].strip()
except:
maf_index_filename = None
index = index_filename = None
if maf_source_type == "user":
#index maf for use here
index, index_filename = maf_utilities.open_or_build_maf_index( input_maf_filename, maf_index_filename, species = [dbkey] )
if index is None:
print >>sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
elif maf_source_type == "cached":
#access existing indexes
index = maf_utilities.maf_index_by_uid( input_maf_filename, mafIndexFile )
if index is None:
print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( input_maf_filename )
sys.exit()
else:
print >>sys.stdout, 'Invalid source type specified: %s' % maf_source_type
sys.exit()
out = open(output_filename, 'w')
num_region = 0
species_summary = {}
total_length = 0
#loop through interval file
for num_region, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_interval_filename, 'r' ), chrom_col = chr_col, start_col = start_col, end_col = end_col, fix_strand = True, return_header = False, return_comments = False ) ):
src = "%s.%s" % ( dbkey, region.chrom )
region_length = region.end - region.start
total_length += region_length
coverage = { dbkey: BitSet( region_length ) }
for block in maf_utilities.get_chopped_blocks_for_region( index, src, region, force_strand='+' ):
#make sure all species are known
for c in block.components:
spec = c.src.split( '.' )[0]
if spec not in coverage: coverage[spec] = BitSet( region_length )
start_offset, alignment = maf_utilities.reduce_block_by_primary_genome( block, dbkey, region.chrom, region.start )
for i in range( len( alignment[dbkey] ) ):
for spec, text in alignment.items():
if text[i] != '-':
coverage[spec].set( start_offset + i )
if summary:
#record summary
for key in coverage.keys():
if key not in species_summary: species_summary[key] = 0
species_summary[key] = species_summary[key] + coverage[key].count_range()
else:
#print coverage for interval
coverage_sum = coverage[dbkey].count_range()
out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), dbkey, coverage_sum, region_length - coverage_sum ) )
keys = coverage.keys()
keys.remove( dbkey )
keys.sort()
for key in keys:
coverage_sum = coverage[key].count_range()
out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), key, coverage_sum, region_length - coverage_sum ) )
if summary:
out.write( "#species\tnucleotides\tcoverage\n" )
for spec in species_summary:
out.write( "%s\t%s\t%.4f\n" % ( spec, species_summary[spec], float( species_summary[spec] ) / total_length ) )
out.close()
print "%i regions were processed with a total length of %i." % ( num_region, total_length )
maf_utilities.remove_temp_index_file( index_filename )
def __main__():
index = index_filename = None
mincols = 0
#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 = maf_utilities.parse_species_option( options.species )
if options.chromCol: chromCol = int( options.chromCol ) - 1
else:
print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
sys.exit()
if options.startCol: startCol = int( options.startCol ) - 1
else:
print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes."
sys.exit()
if options.endCol: endCol = int( options.endCol ) - 1
else:
print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes."
sys.exit()
if options.strandCol: strandCol = int( options.strandCol ) - 1
else:
strandCol = -1
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()
#Finish parsing command line
#Open indexed access to MAFs
if options.mafType:
if options.indexLocation:
index = maf_utilities.maf_index_by_uid( options.mafType, options.indexLocation )
else:
index = maf_utilities.maf_index_by_uid( options.mafType, options.mafIndexFile )
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 = maf_utilities.open_or_build_maf_index( options.mafFile, options.mafIndex, 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()
#Create MAF writter
out = bx.align.maf.Writer( open(output_file, "w") )
#Iterate over input regions
num_blocks = 0
num_regions = None
for num_regions, 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 ) ):
src = "%s.%s" % ( dbkey, region.chrom )
for block in maf_utilities.get_chopped_blocks_for_region( index, src, region, species, mincols ):
out.write( block )
num_blocks += 1
#Close output MAF
out.close()
#remove index file if created during run
maf_utilities.remove_temp_index_file( index_filename )
if num_blocks:
print "%i MAF blocks extracted for %i regions." % ( num_blocks, ( num_regions + 1 ) )
elif num_regions is not None:
print "No MAF blocks could be extracted for %i regions." % ( num_regions + 1 )
else:
print "No valid regions have been provided."
