def __main__():
try:
maf_reader = maf.Reader( open( sys.argv[1] ) )
except Exception as e:
maf_utilities.tool_fail( "Error opening MAF: %s" % e )
try:
out = maf.Writer( open( sys.argv[2], "w") )
except Exception as e:
maf_utilities.tool_fail( "Error opening file for output: %s" % e )
try:
collapse_columns = string_as_bool( sys.argv[3] )
except Exception as e:
maf_utilities.tool_fail( "Error determining collapse columns value: %s" % e )
start_count = 0
end_count = 0
for start_count, start_block in enumerate( maf_reader ):
for block in maf_utilities.iter_blocks_split_by_species( start_block ):
if collapse_columns:
block.remove_all_gap_columns()
out.write( block )
end_count += 1
out.close()
if end_count:
print "%i alignment blocks created from %i original blocks." % ( end_count, start_count + 1 )
else:
print "No alignment blocks were created."
def __main__():
input_filename = sys.argv[1]
output_filename = sys.argv[2]
output_id = sys.argv[3]
# where to store files that become additional output
database_tmp_dir = sys.argv[4]
primary_spec = sys.argv[5]
species = sys.argv[6].split( ',' )
all_species = sys.argv[7].split( ',' )
partial = sys.argv[8]
keep_gaps = sys.argv[9]
out_files = {}
if "None" in species:
species = []
if primary_spec not in species:
species.append( primary_spec )
if primary_spec not in all_species:
all_species.append( primary_spec )
all_species.sort()
for spec in species:
if spec == primary_spec:
out_files[ spec ] = open( output_filename, 'wb+' )
else:
out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_interval_%s' % ( output_id, spec, spec ) ), 'wb+' )
out_files[ spec ].write( '#chrom\tstart\tend\tstrand\tscore\tname\t%s\n' % ( '\t'.join( all_species ) ) )
num_species = len( all_species )
file_in = open( input_filename, 'r' )
maf_reader = maf.Reader( file_in )
for i, m in enumerate( maf_reader ):
for j, block in enumerate( maf_utilities.iter_blocks_split_by_species( m ) ):
if len( block.components ) < num_species and partial == "partial_disallowed":
continue
sequences = {}
for c in block.components:
spec, chrom = maf_utilities.src_split( c.src )
if keep_gaps == 'remove_gaps':
sequences[ spec ] = c.text.replace( '-', '' )
else:
sequences[ spec ] = c.text
sequences = '\t'.join( [ sequences.get( _, '' ) for _ in all_species ] )
for spec in species:
c = block.get_component_by_src_start( spec )
if c is not None:
spec2, chrom = maf_utilities.src_split( c.src )
assert spec2 == spec, Exception( 'Species name inconsistancy found in component: %s != %s' % ( spec, spec2 ) )
out_files[ spec ].write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( chrom, c.forward_strand_start, c.forward_strand_end, c.strand, m.score, "%s_%s_%s" % (spec, i, j), sequences ) )
file_in.close()
for file_out in out_files.values():
file_out.close()
def __main__():
try:
species = maf_utilities.parse_species_option(sys.argv[1])
except Exception as e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
try:
input_filename = sys.argv[2]
except Exception as e:
maf_utilities.tool_fail("Error reading MAF filename: %s" % e)
try:
file_out = open(sys.argv[3], 'w')
except Exception as e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
if species:
print "Restricted to species: %s" % ', '.join(species)
else:
print "Not restricted to species."
if not species:
try:
species = maf_utilities.get_species_in_maf(input_filename)
except Exception as e:
maf_utilities.tool_fail(
"Error determining species in input MAF: %s" % e)
for spec in species:
file_out.write(">" + spec + "\n")
try:
for start_block in maf.Reader(open(input_filename, 'r')):
for block in maf_utilities.iter_blocks_split_by_species(
start_block):
block.remove_all_gap_columns() # remove extra gaps
component = block.get_component_by_src_start(
spec
) # blocks only have one occurrence of a particular species, so this is safe
if component:
file_out.write(component.text)
else:
file_out.write("-" * block.text_size)
except Exception as e:
maf_utilities.tool_fail(
"Your MAF file appears to be malformed: %s" % e)
file_out.write("\n")
file_out.close()
def __main__():
try:
species = maf_utilities.parse_species_option(sys.argv[1])
except Exception as e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
try:
input_filename = sys.argv[2]
except Exception as e:
maf_utilities.tool_fail("Error reading MAF filename: %s" % e)
try:
file_out = open(sys.argv[3], 'w')
except Exception as e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
if species:
print("Restricted to species: %s" % ', '.join(species))
else:
print("Not restricted to species.")
if not species:
try:
species = maf_utilities.get_species_in_maf(input_filename)
except Exception as e:
maf_utilities.tool_fail("Error determining species in input MAF: %s" % e)
for spec in species:
file_out.write(">" + spec + "\n")
try:
for start_block in maf.Reader(open(input_filename, 'r')):
for block in maf_utilities.iter_blocks_split_by_species(start_block):
block.remove_all_gap_columns() # remove extra gaps
component = block.get_component_by_src_start(spec) # blocks only have one occurrence of a particular species, so this is safe
if component:
file_out.write(component.text)
else:
file_out.write("-" * block.text_size)
except Exception as e:
maf_utilities.tool_fail("Your MAF file appears to be malformed: %s" % e)
file_out.write("\n")
file_out.close()
if species:
print "Restricted to species: %s" % ", ".join(species)
else:
print "Not restricted to species."
if not species:
try:
species = maf_utilities.get_species_in_maf(input_filename)
except Exception, e:
maf_utilities.tool_fail("Error determining species in input MAF: %s" % e)
for spec in species:
file_out.write(">" + spec + "\n")
try:
for start_block in maf.Reader(open(input_filename, "r")):
for block in maf_utilities.iter_blocks_split_by_species(start_block):
block.remove_all_gap_columns() # remove extra gaps
component = block.get_component_by_src_start(
spec
) # blocks only have one occurrence of a particular species, so this is safe
if component:
file_out.write(component.text)
else:
file_out.write("-" * block.text_size)
except Exception, e:
maf_utilities.tool_fail("Your MAF file appears to be malformed: %s" % e)
file_out.write("\n")
file_out.close()
if __name__ == "__main__":
print "Restricted to species: %s" % ', '.join(species)
else:
print "Not restricted to species."
if not species:
try:
species = maf_utilities.get_species_in_maf(input_filename)
except Exception, e:
maf_utilities.tool_fail(
"Error determining species in input MAF: %s" % e)
for spec in species:
file_out.write(">" + spec + "\n")
try:
for start_block in maf.Reader(open(input_filename, 'r')):
for block in maf_utilities.iter_blocks_split_by_species(
start_block):
block.remove_all_gap_columns() #remove extra gaps
component = block.get_component_by_src_start(
spec
) #blocks only have one occurrence of a particular species, so this is safe
if component:
file_out.write(component.text)
else:
file_out.write("-" * block.text_size)
except Exception, e:
maf_utilities.tool_fail(
"Your MAF file appears to be malformed: %s" % e)
file_out.write("\n")
file_out.close()
def __main__():
index = index_filename = None
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
if options.dbkey:
dbkey = options.dbkey
else:
dbkey = None
if dbkey in [None, "?"]:
maf_utilities.tool_fail(
"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."
)
species = maf_utilities.parse_species_option(options.species)
if options.chromCol:
chromCol = int(options.chromCol) - 1
else:
maf_utilities.tool_fail(
"Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
)
if options.startCol:
startCol = int(options.startCol) - 1
else:
maf_utilities.tool_fail(
"Start column not set, click the pencil icon in the history item to set the metadata attributes."
)
if options.endCol:
endCol = int(options.endCol) - 1
else:
maf_utilities.tool_fail(
"End column not set, click the pencil icon in the history item to set the metadata attributes."
)
if options.strandCol:
strandCol = int(options.strandCol) - 1
else:
strandCol = -1
if options.interval_file:
interval_file = options.interval_file
else:
maf_utilities.tool_fail("Input interval file has not been specified.")
if options.output_file:
output_file = options.output_file
else:
maf_utilities.tool_fail("Output file has not been specified.")
split_blocks_by_species = remove_all_gap_columns = False
if options.split_blocks_by_species and options.split_blocks_by_species == 'split_blocks_by_species':
split_blocks_by_species = True
if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns':
remove_all_gap_columns = True
else:
remove_all_gap_columns = True
# 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:
maf_utilities.tool_fail(
"The MAF source specified (%s) appears to be invalid." %
(options.mafType))
elif options.mafFile:
index, index_filename = maf_utilities.open_or_build_maf_index(
options.mafFile, options.mafIndex, species=[dbkey])
if index is None:
maf_utilities.tool_fail("Your MAF file appears to be malformed.")
else:
maf_utilities.tool_fail(
"Desired source MAF type has not been specified.")
# 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),
chrom_col=chromCol,
start_col=startCol,
end_col=endCol,
strand_col=strandCol,
fix_strand=True,
return_header=False,
return_comments=False)): # noqa: B007
src = maf_utilities.src_merge(dbkey, region.chrom)
for block in index.get_as_iterator(src, region.start, region.end):
if split_blocks_by_species:
blocks = [
new_block for new_block in
maf_utilities.iter_blocks_split_by_species(block)
if maf_utilities.component_overlaps_region(
new_block.get_component_by_src_start(dbkey), region)
]
else:
blocks = [block]
for block in blocks:
block = maf_utilities.chop_block_by_region(block, src, region)
if block is not None:
if species is not None:
block = block.limit_to_species(species)
block = maf_utilities.orient_block_by_region(
block, src, region)
if remove_all_gap_columns:
block.remove_all_gap_columns()
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.")
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 Exception:
print(
"You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file.",
file=sys.stderr)
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 Exception:
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("Your MAF file appears to be malformed.", file=sys.stderr)
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("The MAF source specified (%s) appears to be invalid." %
(input_maf_filename),
file=sys.stderr)
sys.exit()
else:
print('Invalid source type specified: %s' % maf_source_type,
file=sys.stdout)
sys.exit()
out = open(output_filename, 'w')
num_region = None
num_bad_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)): # noqa: B007
src = "%s.%s" % (dbkey, region.chrom)
region_length = region.end - region.start
if region_length < 1:
num_bad_region += 1
continue
total_length += region_length
coverage = {dbkey: BitSet(region_length)}
for block in index.get_as_iterator(src, region.start, region.end):
for spec in maf_utilities.get_species_in_block(block):
if spec not in coverage:
coverage[spec] = BitSet(region_length)
for block in maf_utilities.iter_blocks_split_by_species(block):
if maf_utilities.component_overlaps_region(
block.get_component_by_src(src), region):
# need to chop and orient the block
block = maf_utilities.orient_block_by_region(
maf_utilities.chop_block_by_region(block, src, region),
src,
region,
force_strand='+')
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 = list(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()
if num_region is not None:
print("%i regions were processed with a total length of %i." %
(num_region + 1, total_length))
if num_bad_region:
print("%i regions were invalid." % (num_bad_region))
maf_utilities.remove_temp_index_file(index_filename)
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("You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file.", file=sys.stderr)
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("Your MAF file appears to be malformed.", file=sys.stderr)
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("The MAF source specified (%s) appears to be invalid." % ( input_maf_filename ), file=sys.stderr)
sys.exit()
else:
print('Invalid source type specified: %s' % maf_source_type, file=sys.stdout)
sys.exit()
out = open(output_filename, 'w')
num_region = None
num_bad_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
if region_length < 1:
num_bad_region += 1
continue
total_length += region_length
coverage = { dbkey: BitSet( region_length ) }
for block in index.get_as_iterator( src, region.start, region.end ):
for spec in maf_utilities.get_species_in_block( block ):
if spec not in coverage:
coverage[spec] = BitSet( region_length )
for block in maf_utilities.iter_blocks_split_by_species( block ):
if maf_utilities.component_overlaps_region( block.get_component_by_src( src ), region ):
# need to chop and orient the block
block = maf_utilities.orient_block_by_region( maf_utilities.chop_block_by_region( block, src, region ), src, region, force_strand='+' )
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 = list(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()
if num_region is not None:
print("%i regions were processed with a total length of %i." % ( num_region + 1, total_length ))
if num_bad_region:
print("%i regions were invalid." % ( num_bad_region ))
maf_utilities.remove_temp_index_file( index_filename )
def __main__():
index = index_filename = None
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
if options.dbkey:
dbkey = options.dbkey
else:
dbkey = None
if dbkey in [None, "?"]:
maf_utilities.tool_fail("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.")
species = maf_utilities.parse_species_option(options.species)
if options.chromCol:
chromCol = int(options.chromCol) - 1
else:
maf_utilities.tool_fail("Chromosome column not set, click the pencil icon in the history item to set the metadata attributes.")
if options.startCol:
startCol = int(options.startCol) - 1
else:
maf_utilities.tool_fail("Start column not set, click the pencil icon in the history item to set the metadata attributes.")
if options.endCol:
endCol = int(options.endCol) - 1
else:
maf_utilities.tool_fail("End column not set, click the pencil icon in the history item to set the metadata attributes.")
if options.strandCol:
strandCol = int(options.strandCol) - 1
else:
strandCol = -1
if options.interval_file:
interval_file = options.interval_file
else:
maf_utilities.tool_fail("Input interval file has not been specified.")
if options.output_file:
output_file = options.output_file
else:
maf_utilities.tool_fail("Output file has not been specified.")
split_blocks_by_species = remove_all_gap_columns = False
if options.split_blocks_by_species and options.split_blocks_by_species == 'split_blocks_by_species':
split_blocks_by_species = True
if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns':
remove_all_gap_columns = True
else:
remove_all_gap_columns = True
# 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:
maf_utilities.tool_fail("The MAF source specified (%s) appears to be invalid." % (options.mafType))
elif options.mafFile:
index, index_filename = maf_utilities.open_or_build_maf_index(options.mafFile, options.mafIndex, species=[dbkey])
if index is None:
maf_utilities.tool_fail("Your MAF file appears to be malformed.")
else:
maf_utilities.tool_fail("Desired source MAF type has not been specified.")
# 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 = maf_utilities.src_merge(dbkey, region.chrom)
for block in index.get_as_iterator(src, region.start, region.end):
if split_blocks_by_species:
blocks = [new_block for new_block in maf_utilities.iter_blocks_split_by_species(block) if maf_utilities.component_overlaps_region(new_block.get_component_by_src_start(dbkey), region)]
else:
blocks = [block]
for block in blocks:
block = maf_utilities.chop_block_by_region(block, src, region)
if block is not None:
if species is not None:
block = block.limit_to_species(species)
block = maf_utilities.orient_block_by_region(block, src, region)
if remove_all_gap_columns:
block.remove_all_gap_columns()
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.")
