def __main__():
input_block_filename = sys.argv[1].strip()
input_maf_filename = sys.argv[2].strip()
output_filename1 = sys.argv[3].strip()
block_col = int(sys.argv[4].strip()) - 1
if block_col < 0:
print >> sys.stderr, "Invalid column specified"
sys.exit(0)
species = maf_utilities.parse_species_option(sys.argv[5].strip())
maf_writer = bx.align.maf.Writer(open(output_filename1, 'w'))
# we want to maintain order of block file and write blocks as many times as they are listed
failed_lines = []
for ctr, line in enumerate(open(input_block_filename, 'r')):
try:
block_wanted = int(line.split("\t")[block_col].strip())
except:
failed_lines.append(str(ctr))
continue
try:
for count, block in enumerate(
bx.align.maf.Reader(open(input_maf_filename, 'r'))):
if count == block_wanted:
if species:
block = block.limit_to_species(species)
maf_writer.write(block)
break
except:
print >> sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
if len(failed_lines) > 0:
print "Failed to extract from %i lines (%s)." % (
len(failed_lines), ",".join(failed_lines))
def main():
species = maf_utilities.parse_species_option(sys.argv[1])
if species:
spec_len = len(species)
else:
spec_len = 0
try:
maf_reader = bx.align.maf.Reader(open(sys.argv[2], 'r'))
maf_writer = bx.align.maf.Writer(open(sys.argv[3], 'w'))
except Exception:
print("Your MAF file appears to be malformed.", file=sys.stderr)
sys.exit()
allow_partial = False
if int(sys.argv[4]):
allow_partial = True
min_species_per_block = int(sys.argv[5])
maf_blocks_kept = 0
for m in maf_reader:
if species:
m = m.limit_to_species(species)
m.remove_all_gap_columns()
spec_in_block_len = len(maf_utilities.get_species_in_block(m))
if (not species or allow_partial or spec_in_block_len == spec_len) and spec_in_block_len > min_species_per_block:
maf_writer.write(m)
maf_blocks_kept += 1
maf_reader.close()
maf_writer.close()
print("Restricted to species: %s." % ", ".join(species))
print("%i MAF blocks have been kept." % maf_blocks_kept)
def __main__():
input_block_filename = sys.argv[1].strip()
input_maf_filename = sys.argv[2].strip()
output_filename1 = sys.argv[3].strip()
block_col = int( sys.argv[4].strip() ) - 1
if block_col < 0:
print >> sys.stderr, "Invalid column specified"
sys.exit(0)
species = maf_utilities.parse_species_option( sys.argv[5].strip() )
maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
# we want to maintain order of block file and write blocks as many times as they are listed
failed_lines = []
for ctr, line in enumerate( open( input_block_filename, 'r' ) ):
try:
block_wanted = int( line.split( "\t" )[block_col].strip() )
except:
failed_lines.append( str( ctr ) )
continue
try:
for count, block in enumerate( bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) ):
if count == block_wanted:
if species:
block = block.limit_to_species( species )
maf_writer.write( block )
break
except:
print >>sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
if len( failed_lines ) > 0:
print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )
def main():
species = maf_utilities.parse_species_option( sys.argv[1] )
if species:
spec_len = len( species )
else:
spec_len = 0
try:
maf_reader = bx.align.maf.Reader( open( sys.argv[2], 'r' ) )
maf_writer = bx.align.maf.Writer( open( sys.argv[3], 'w' ) )
except:
print("Your MAF file appears to be malformed.", file=sys.stderr)
sys.exit()
allow_partial = False
if int( sys.argv[4] ):
allow_partial = True
min_species_per_block = int( sys.argv[5] )
maf_blocks_kept = 0
for m in maf_reader:
if species:
m = m.limit_to_species( species )
m.remove_all_gap_columns()
spec_in_block_len = len( maf_utilities.get_species_in_block( m ) )
if ( not species or allow_partial or spec_in_block_len == spec_len ) and spec_in_block_len > min_species_per_block:
maf_writer.write( m )
maf_blocks_kept += 1
maf_reader.close()
maf_writer.close()
print("Restricted to species: %s." % ", ".join( species ))
print("%i MAF blocks have been kept." % maf_blocks_kept)
def main():
#Read command line arguments
try:
script_file = sys.argv.pop(1)
maf_file = sys.argv.pop(1)
out_file = sys.argv.pop(1)
additional_files_path = sys.argv.pop(1)
species = maf_utilities.parse_species_option(sys.argv.pop(1))
min_size = int(sys.argv.pop(1))
max_size = int(sys.argv.pop(1))
if max_size < 1:
max_size = sys.maxint
min_species_per_block = int(sys.argv.pop(1))
exclude_incomplete_blocks = int(sys.argv.pop(1))
if species:
num_species = len(species)
else:
num_species = len(sys.argv.pop(1).split(','))
except:
print >> sys.stderr, "One or more arguments is missing.\nUsage: maf_filter.py maf_filter_file input_maf output_maf path_to_save_debug species_to_keep"
sys.exit()
#Open input and output MAF files
try:
maf_reader = bx.align.maf.Reader(open(maf_file, 'r'))
maf_writer = bx.align.maf.Writer(open(out_file, 'w'))
except:
print >> sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
#Save script file for debuging/verification info later
os.mkdir(additional_files_path)
shutil.copy(script_file, os.path.join(additional_files_path, 'debug.txt'))
#Loop through blocks, running filter on each
#'maf_block' and 'ret_val' are used/shared in the provided code file
#'ret_val' should be set to True if the block is to be kept
i = 0
blocks_kept = 0
for i, maf_block in enumerate(maf_reader):
if min_size <= maf_block.text_size <= max_size:
local = {'maf_block': maf_block, 'ret_val': False}
execfile(script_file, {}, local)
if local['ret_val']:
#Species limiting must be done after filters as filters could be run on non-requested output species
if species:
maf_block = maf_block.limit_to_species(species)
if len(maf_block.components) >= min_species_per_block and (
not exclude_incomplete_blocks
or len(maf_block.components) >= num_species):
maf_writer.write(maf_block)
blocks_kept += 1
maf_writer.close()
maf_reader.close()
if i == 0:
print "Your file contains no valid maf_blocks."
else:
print 'Kept %s of %s blocks (%.2f%%).' % (
blocks_kept, i + 1, float(blocks_kept) / float(i + 1) * 100.0)
def main():
# Read command line arguments
try:
script_file = sys.argv.pop(1)
maf_file = sys.argv.pop(1)
out_file = sys.argv.pop(1)
additional_files_path = sys.argv.pop(1)
species = maf_utilities.parse_species_option(sys.argv.pop(1))
min_size = int(sys.argv.pop(1))
max_size = int(sys.argv.pop(1))
if max_size < 1:
max_size = sys.maxint
min_species_per_block = int(sys.argv.pop(1))
exclude_incomplete_blocks = int(sys.argv.pop(1))
if species:
num_species = len(species)
else:
num_species = len(sys.argv.pop(1).split(","))
except:
print >> sys.stderr, "One or more arguments is missing.\nUsage: maf_filter.py maf_filter_file input_maf output_maf path_to_save_debug species_to_keep"
sys.exit()
# Open input and output MAF files
try:
maf_reader = bx.align.maf.Reader(open(maf_file, "r"))
maf_writer = bx.align.maf.Writer(open(out_file, "w"))
except:
print >> sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
# Save script file for debuging/verification info later
os.mkdir(additional_files_path)
shutil.copy(script_file, os.path.join(additional_files_path, "debug.txt"))
# Loop through blocks, running filter on each
#'maf_block' and 'ret_val' are used/shared in the provided code file
#'ret_val' should be set to True if the block is to be kept
i = 0
blocks_kept = 0
for i, maf_block in enumerate(maf_reader):
if min_size <= maf_block.text_size <= max_size:
local = {"maf_block": maf_block, "ret_val": False}
execfile(script_file, {}, local)
if local["ret_val"]:
# Species limiting must be done after filters as filters could be run on non-requested output species
if species:
maf_block = maf_block.limit_to_species(species)
if len(maf_block.components) >= min_species_per_block and (
not exclude_incomplete_blocks or len(maf_block.components) >= num_species
):
maf_writer.write(maf_block)
blocks_kept += 1
maf_writer.close()
maf_reader.close()
if i == 0:
print "Your file contains no valid maf_blocks."
else:
print "Kept %s of %s blocks (%.2f%%)." % (blocks_kept, i + 1, float(blocks_kept) / float(i + 1) * 100.0)
def __main__():
try:
maf_reader = maf.Reader(open(sys.argv[1]))
except Exception as e:
maf_utilities.tool_fail("Error opening input MAF: %s" % e)
try:
file_out = open(sys.argv[2], 'w')
except Exception as e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
try:
species = maf_utilities.parse_species_option(sys.argv[3])
if species:
num_species = len(species)
else:
num_species = 0
except Exception as e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
try:
partial = sys.argv[4]
except Exception as e:
maf_utilities.tool_fail("Error determining keep partial value: %s" % e)
if species:
print("Restricted to species: %s" % ', '.join(species))
else:
print("Not restricted to species.")
for block_num, block in enumerate(maf_reader):
if species:
block = block.limit_to_species(species)
if len(maf_utilities.get_species_in_block(
block)) < num_species and partial == "partial_disallowed":
continue
spec_counts = {}
for component in block.components:
spec, chrom = maf_utilities.src_split(component.src)
if spec not in spec_counts:
spec_counts[spec] = 0
else:
spec_counts[spec] += 1
file_out.write("%s\n" % maf_utilities.get_fasta_header(
component, {
'block_index': block_num,
'species': spec,
'sequence_index': spec_counts[spec]
},
suffix="%s_%i_%i" % (spec, block_num, spec_counts[spec])))
file_out.write("%s\n" % component.text)
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()
def __main__():
try:
maf_reader = maf.Reader(open(sys.argv[1]))
except Exception as e:
maf_utilities.tool_fail("Error opening input MAF: %s" % e)
try:
file_out = open(sys.argv[2], 'w')
except Exception as e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
try:
species = maf_utilities.parse_species_option(sys.argv[3])
if species:
num_species = len(species)
else:
num_species = 0
except Exception as e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
try:
partial = sys.argv[4]
except Exception as e:
maf_utilities.tool_fail("Error determining keep partial value: %s" % e)
if species:
print("Restricted to species: %s" % ', '.join(species))
else:
print("Not restricted to species.")
for block_num, block in enumerate(maf_reader):
if species:
block = block.limit_to_species(species)
if len(maf_utilities.get_species_in_block(block)) < num_species and partial == "partial_disallowed":
continue
spec_counts = {}
for component in block.components:
spec, chrom = maf_utilities.src_split(component.src)
if spec not in spec_counts:
spec_counts[spec] = 0
else:
spec_counts[spec] += 1
d = OrderedDict([('block_index', block_num), ('species', spec), ('sequence_index', spec_counts[spec])])
file_out.write("%s\n" % maf_utilities.get_fasta_header(component, d, suffix="%s_%i_%i" % (spec, block_num, spec_counts[spec])))
file_out.write("%s\n" % component.text)
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()
def __main__():
#Parse Command Line
input_file = sys.argv.pop( 1 )
output_file = sys.argv.pop( 1 )
species = maf_utilities.parse_species_option( sys.argv.pop( 1 ) )
try:
maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )
except:
print sys.stderr, "Unable to open output file"
sys.exit()
try:
count = 0
for count, maf in enumerate( bx.align.maf.Reader( open( input_file ) ) ):
maf = maf.reverse_complement()
if species:
maf = maf.limit_to_species( species )
maf_writer.write( maf )
except:
print >>sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
print "%i regions were reverse complemented." % count
maf_writer.close()
def __main__():
# Parse Command Line
input_file = sys.argv.pop(1)
output_file = sys.argv.pop(1)
species = maf_utilities.parse_species_option(sys.argv.pop(1))
try:
maf_writer = bx.align.maf.Writer(open(output_file, 'w'))
except Exception:
print(sys.stderr, "Unable to open output file")
sys.exit()
try:
count = 0
for count, maf in enumerate(bx.align.maf.Reader(open(input_file))): # noqa: B007
maf = maf.reverse_complement()
if species:
maf = maf.limit_to_species(species)
maf_writer.write(maf)
except Exception:
print("Your MAF file appears to be malformed.", file=sys.stderr)
sys.exit()
print("%i regions were reverse complemented." % count)
maf_writer.close()
def __main__():
try:
species = maf_utilities.parse_species_option(sys.argv[1])
except Exception, e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
from bx.align import maf
from galaxy.tools.util import maf_utilities
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
try:
maf_reader = maf.Reader( open( sys.argv[1] ) )
except Exception, e:
maf_utilities.tool_fail( "Error opening input MAF: %s" % e )
try:
file_out = open( sys.argv[2], 'w' )
except Exception, e:
maf_utilities.tool_fail( "Error opening file for output: %s" % e )
try:
species = maf_utilities.parse_species_option( sys.argv[3] )
if species:
num_species = len( species )
else:
num_species = 0
except Exception, e:
maf_utilities.tool_fail( "Error determining species value: %s" % e )
try:
partial = sys.argv[4]
except Exception, e:
maf_utilities.tool_fail( "Error determining keep partial value: %s" % e )
if species:
print "Restricted to species: %s" % ', '.join( species )
else:
print "Not restricted to species."
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.")
def __main__():
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
mincols = 0
strand_col = -1
if options.dbkey:
primary_species = options.dbkey
else:
primary_species = None
if primary_species in [None, "?", "None"]:
stop_err("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.")
include_primary = True
secondary_species = maf_utilities.parse_species_option(options.species)
if secondary_species:
species = list(secondary_species) # make copy of species list
if primary_species in secondary_species:
secondary_species.remove(primary_species)
else:
include_primary = False
else:
species = None
if options.interval_file:
interval_file = options.interval_file
else:
stop_err("Input interval file has not been specified.")
if options.output_file:
output_file = options.output_file
else:
stop_err("Output file has not been specified.")
if not options.geneBED:
if options.chromCol:
chr_col = int(options.chromCol) - 1
else:
stop_err("Chromosome column not set, click the pencil icon in the history item to set the metadata attributes.")
if options.startCol:
start_col = int(options.startCol) - 1
else:
stop_err("Start column not set, click the pencil icon in the history item to set the metadata attributes.")
if options.endCol:
end_col = int(options.endCol) - 1
else:
stop_err("End column not set, click the pencil icon in the history item to set the metadata attributes.")
if options.strandCol:
strand_col = int(options.strandCol) - 1
mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir
overwrite_with_gaps = True
if options.overwrite_with_gaps and options.overwrite_with_gaps.lower() == 'false':
overwrite_with_gaps = False
# Finish parsing command line
# get index for mafs based on type
index = index_filename = None
# using specified uid for locally cached
if options.mafSourceType.lower() in ["cached"]:
index = maf_utilities.maf_index_by_uid(options.mafSource, mafIndexFile)
if index is None:
stop_err("The MAF source specified (%s) appears to be invalid." % (options.mafSource))
elif options.mafSourceType.lower() in ["user"]:
# index maf for use here, need to remove index_file when finished
index, index_filename = maf_utilities.open_or_build_maf_index(options.mafSource, options.mafIndex, species=[primary_species])
if index is None:
stop_err("Your MAF file appears to be malformed.")
else:
stop_err("Invalid MAF source type specified.")
# open output file
output = open(output_file, "w")
if options.geneBED:
region_enumerator = maf_utilities.line_enumerator(open(interval_file, "r").readlines())
else:
region_enumerator = enumerate(bx.intervals.io.NiceReaderWrapper(
open(interval_file, 'r'), chrom_col=chr_col, start_col=start_col,
end_col=end_col, strand_col=strand_col, fix_strand=True,
return_header=False, return_comments=False))
# Step through intervals
regions_extracted = 0
line_count = 0
for line_count, line in region_enumerator:
try:
if options.geneBED: # Process as Gene BED
try:
starts, ends, fields = maf_utilities.get_starts_ends_fields_from_gene_bed(line)
# create spliced alignment object
alignment = maf_utilities.get_spliced_region_alignment(
index, primary_species, fields[0], starts, ends,
strand='+', species=species, mincols=mincols,
overwrite_with_gaps=overwrite_with_gaps)
primary_name = secondary_name = fields[3]
alignment_strand = fields[5]
except Exception as e:
print("Error loading exon positions from input line %i: %s" % (line_count, e))
continue
else: # Process as standard intervals
try:
# create spliced alignment object
alignment = maf_utilities.get_region_alignment(
index, primary_species, line.chrom, line.start,
line.end, strand='+', species=species, mincols=mincols,
overwrite_with_gaps=overwrite_with_gaps)
primary_name = "%s(%s):%s-%s" % (line.chrom, line.strand, line.start, line.end)
secondary_name = ""
alignment_strand = line.strand
except Exception as e:
print("Error loading region positions from input line %i: %s" % (line_count, e))
continue
# Write alignment to output file
# Output primary species first, if requested
if include_primary:
output.write(">%s.%s\n" % (primary_species, primary_name))
if alignment_strand == "-":
output.write(alignment.get_sequence_reverse_complement(primary_species))
else:
output.write(alignment.get_sequence(primary_species))
output.write("\n")
# Output all remainging species
for spec in secondary_species or alignment.get_species_names(skip=primary_species):
if secondary_name:
output.write(">%s.%s\n" % (spec, secondary_name))
else:
output.write(">%s\n" % (spec))
if alignment_strand == "-":
output.write(alignment.get_sequence_reverse_complement(spec))
else:
output.write(alignment.get_sequence(spec))
output.write("\n")
output.write("\n")
regions_extracted += 1
except Exception as e:
print("Unexpected error from input line %i: %s" % (line_count, e))
continue
# close output file
output.close()
# remove index file if created during run
maf_utilities.remove_temp_index_file(index_filename)
# Print message about success for user
if regions_extracted > 0:
print("%i regions were processed successfully." % (regions_extracted))
else:
print("No regions were processed successfully.")
if line_count > 0 and options.geneBED:
print("This tool requires your input file to conform to the 12 column BED standard.")
def __main__():
try:
species = maf_utilities.parse_species_option(sys.argv[1])
except Exception, e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
def __main__():
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
mincols = 0
strand_col = -1
if options.dbkey:
primary_species = options.dbkey
else:
primary_species = None
if primary_species in [None, "?", "None"]:
stop_err(
"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."
)
include_primary = True
secondary_species = maf_utilities.parse_species_option(options.species)
if secondary_species:
species = list(secondary_species) # make copy of species list
if primary_species in secondary_species:
secondary_species.remove(primary_species)
else:
include_primary = False
else:
species = None
if options.interval_file:
interval_file = options.interval_file
else:
stop_err("Input interval file has not been specified.")
if options.output_file:
output_file = options.output_file
else:
stop_err("Output file has not been specified.")
if not options.geneBED:
if options.chromCol:
chr_col = int(options.chromCol) - 1
else:
stop_err(
"Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
)
if options.startCol:
start_col = int(options.startCol) - 1
else:
stop_err("Start column not set, click the pencil icon in the history item to set the metadata attributes.")
if options.endCol:
end_col = int(options.endCol) - 1
else:
stop_err("End column not set, click the pencil icon in the history item to set the metadata attributes.")
if options.strandCol:
strand_col = int(options.strandCol) - 1
mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir
# Finish parsing command line
# get index for mafs based on type
index = index_filename = None
# using specified uid for locally cached
if options.mafSourceType.lower() in ["cached"]:
index = maf_utilities.maf_index_by_uid(options.mafSource, mafIndexFile)
if index is None:
stop_err("The MAF source specified (%s) appears to be invalid." % (options.mafSource))
elif options.mafSourceType.lower() in ["user"]:
# index maf for use here, need to remove index_file when finished
index, index_filename = maf_utilities.open_or_build_maf_index(
options.mafSource, options.mafIndex, species=[primary_species]
)
if index is None:
stop_err("Your MAF file appears to be malformed.")
else:
stop_err("Invalid MAF source type specified.")
# open output file
output = open(output_file, "w")
if options.geneBED:
region_enumerator = maf_utilities.line_enumerator(open(interval_file, "r").readlines())
else:
region_enumerator = enumerate(
bx.intervals.io.NiceReaderWrapper(
open(interval_file, "r"),
chrom_col=chr_col,
start_col=start_col,
end_col=end_col,
strand_col=strand_col,
fix_strand=True,
return_header=False,
return_comments=False,
)
)
# Step through intervals
regions_extracted = 0
line_count = 0
for line_count, line in region_enumerator:
try:
if options.geneBED: # Process as Gene BED
try:
starts, ends, fields = maf_utilities.get_starts_ends_fields_from_gene_bed(line)
# create spliced alignment object
alignment = maf_utilities.get_spliced_region_alignment(
index, primary_species, fields[0], starts, ends, strand="+", species=species, mincols=mincols
)
primary_name = secondary_name = fields[3]
alignment_strand = fields[5]
except Exception, e:
print "Error loading exon positions from input line %i: %s" % (line_count, e)
continue
else: # Process as standard intervals
try:
# create spliced alignment object
alignment = maf_utilities.get_region_alignment(
index,
primary_species,
line.chrom,
line.start,
line.end,
strand="+",
species=species,
mincols=mincols,
)
primary_name = "%s(%s):%s-%s" % (line.chrom, line.strand, line.start, line.end)
secondary_name = ""
alignment_strand = line.strand
except Exception, e:
print "Error loading region positions from input line %i: %s" % (line_count, e)
continue
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."
def __main__():
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
mincols = 0
strand_col = -1
if options.dbkey:
primary_species = options.dbkey
else:
primary_species = None
if primary_species in [None, "?", "None"]:
stop_err(
"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."
)
include_primary = True
secondary_species = maf_utilities.parse_species_option(options.species)
if secondary_species:
species = list(secondary_species) # make copy of species list
if primary_species in secondary_species:
secondary_species.remove(primary_species)
else:
include_primary = False
else:
species = None
if options.interval_file:
interval_file = options.interval_file
else:
stop_err("Input interval file has not been specified.")
if options.output_file:
output_file = options.output_file
else:
stop_err("Output file has not been specified.")
if not options.geneBED:
if options.chromCol:
chr_col = int(options.chromCol) - 1
else:
stop_err(
"Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
)
if options.startCol:
start_col = int(options.startCol) - 1
else:
stop_err(
"Start column not set, click the pencil icon in the history item to set the metadata attributes."
)
if options.endCol:
end_col = int(options.endCol) - 1
else:
stop_err(
"End column not set, click the pencil icon in the history item to set the metadata attributes."
)
if options.strandCol:
strand_col = int(options.strandCol) - 1
mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir
overwrite_with_gaps = True
if options.overwrite_with_gaps and options.overwrite_with_gaps.lower(
) == 'false':
overwrite_with_gaps = False
# Finish parsing command line
# get index for mafs based on type
index = index_filename = None
# using specified uid for locally cached
if options.mafSourceType.lower() in ["cached"]:
index = maf_utilities.maf_index_by_uid(options.mafSource, mafIndexFile)
if index is None:
stop_err("The MAF source specified (%s) appears to be invalid." %
(options.mafSource))
elif options.mafSourceType.lower() in ["user"]:
# index maf for use here, need to remove index_file when finished
index, index_filename = maf_utilities.open_or_build_maf_index(
options.mafSource, options.mafIndex, species=[primary_species])
if index is None:
stop_err("Your MAF file appears to be malformed.")
else:
stop_err("Invalid MAF source type specified.")
# open output file
output = open(output_file, "w")
if options.geneBED:
region_enumerator = maf_utilities.line_enumerator(
open(interval_file, "r").readlines())
else:
region_enumerator = enumerate(
bx.intervals.io.NiceReaderWrapper(open(interval_file, 'r'),
chrom_col=chr_col,
start_col=start_col,
end_col=end_col,
strand_col=strand_col,
fix_strand=True,
return_header=False,
return_comments=False))
# Step through intervals
regions_extracted = 0
line_count = 0
for line_count, line in region_enumerator:
try:
if options.geneBED: # Process as Gene BED
try:
starts, ends, fields = maf_utilities.get_starts_ends_fields_from_gene_bed(
line)
# create spliced alignment object
alignment = maf_utilities.get_spliced_region_alignment(
index,
primary_species,
fields[0],
starts,
ends,
strand='+',
species=species,
mincols=mincols,
overwrite_with_gaps=overwrite_with_gaps)
primary_name = secondary_name = fields[3]
alignment_strand = fields[5]
except Exception, e:
print "Error loading exon positions from input line %i: %s" % (
line_count, e)
continue
else: # Process as standard intervals
try:
# create spliced alignment object
alignment = maf_utilities.get_region_alignment(
index,
primary_species,
line.chrom,
line.start,
line.end,
strand='+',
species=species,
mincols=mincols,
overwrite_with_gaps=overwrite_with_gaps)
primary_name = "%s(%s):%s-%s" % (line.chrom, line.strand,
line.start, line.end)
secondary_name = ""
alignment_strand = line.strand
except Exception, e:
print "Error loading region positions from input line %i: %s" % (
line_count, e)
continue
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.")
