mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 12:13:33 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
72 lines
2.5 KiB
Python
72 lines
2.5 KiB
Python
#!/usr/bin/env python
|
|
|
|
"""
|
|
Read a maf and output intervals for specified list of species.
|
|
"""
|
|
import os
|
|
import sys
|
|
|
|
from bx.align import maf
|
|
|
|
from galaxy.tools.util import maf_utilities
|
|
|
|
|
|
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, 'w+')
|
|
else:
|
|
out_files[spec] = open(os.path.join(database_tmp_dir, 'primary_%s_%s_visible_interval_%s' % (output_id, spec, spec)), 'w+')
|
|
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)
|
|
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()
|
|
|
|
|
|
if __name__ == "__main__":
|
|
__main__()
|