mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 12:13:33 +08:00
60 lines
2.7 KiB
Python
60 lines
2.7 KiB
Python
# Dan Blankenberg
|
|
# This script checks maf_index.loc file for inconsistencies between what is listed as available and what is really available.
|
|
# Make sure that required dependencies (e.g. galaxy_root/lib) are included in your PYTHONPATH
|
|
|
|
import sys
|
|
|
|
import bx.align.maf
|
|
|
|
from galaxy.tools.util import maf_utilities
|
|
|
|
assert sys.version_info[:2] >= (2, 6)
|
|
|
|
|
|
def __main__():
|
|
index_location_file = sys.argv[1]
|
|
for i, line in enumerate(open(index_location_file)):
|
|
try:
|
|
if line.startswith("#"):
|
|
continue
|
|
display_name, uid, indexed_for_species, species_exist, maf_files = line.rstrip().split("\t")
|
|
indexed_for_species = indexed_for_species.split(",")
|
|
species_exist = species_exist.split(",")
|
|
maf_files = maf_files.split(",")
|
|
species_indexed_in_maf = []
|
|
species_found_in_maf = []
|
|
for maf_file in maf_files:
|
|
indexed_maf = bx.align.maf.MAFIndexedAccess(maf_file, keep_open=True, parse_e_rows=False)
|
|
for key in indexed_maf.indexes.indexes.keys():
|
|
spec = maf_utilities.src_split(key)[0]
|
|
if spec not in species_indexed_in_maf:
|
|
species_indexed_in_maf.append(spec)
|
|
while True: # reading entire maf set will take some time
|
|
block = indexed_maf.read_at_current_offset(indexed_maf.f)
|
|
if block is None:
|
|
break
|
|
for comp in block.components:
|
|
spec = maf_utilities.src_split(comp.src)[0]
|
|
if spec not in species_found_in_maf:
|
|
species_found_in_maf.append(spec)
|
|
# indexed species
|
|
for spec in indexed_for_species:
|
|
if spec not in species_indexed_in_maf:
|
|
print(f"Line {i}, {uid} claims to be indexed for {spec}, but indexes do not exist.")
|
|
for spec in species_indexed_in_maf:
|
|
if spec not in indexed_for_species:
|
|
print(f"Line {i}, {uid} is indexed for {spec}, but is not listed in loc file.")
|
|
# existing species
|
|
for spec in species_exist:
|
|
if spec not in species_found_in_maf:
|
|
print(f"Line {i}, {uid} claims to have blocks for {spec}, but was not found in MAF files.")
|
|
for spec in species_found_in_maf:
|
|
if spec not in species_exist:
|
|
print(f"Line {i}, {uid} contains {spec}, but is not listed in loc file.")
|
|
except Exception as e:
|
|
print(f"Line {i} is invalid: {e}")
|
|
|
|
|
|
if __name__ == "__main__":
|
|
__main__()
|