mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +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
60 lines
2.7 KiB
Python
60 lines
2.7 KiB
Python
# Dan Blankenberg
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# This script checks maf_index.loc file for inconsistencies between what is listed as available and what is really available.
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# Make sure that required dependencies (e.g. galaxy_root/lib) are included in your PYTHONPATH
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import sys
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import bx.align.maf
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from galaxy.tools.util import maf_utilities
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assert sys.version_info[:2] >= (2, 6)
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def __main__():
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index_location_file = sys.argv[1]
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for i, line in enumerate(open(index_location_file)):
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try:
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if line.startswith('#'):
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continue
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display_name, uid, indexed_for_species, species_exist, maf_files = line.rstrip().split('\t')
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indexed_for_species = indexed_for_species.split(',')
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species_exist = species_exist.split(',')
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maf_files = maf_files.split(',')
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species_indexed_in_maf = []
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species_found_in_maf = []
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for maf_file in maf_files:
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indexed_maf = bx.align.maf.MAFIndexedAccess(maf_file, keep_open=True, parse_e_rows=False)
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for key in indexed_maf.indexes.indexes.keys():
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spec = maf_utilities.src_split(key)[0]
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if spec not in species_indexed_in_maf:
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species_indexed_in_maf.append(spec)
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while True: # reading entire maf set will take some time
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block = indexed_maf.read_at_current_offset(indexed_maf.f)
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if block is None:
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break
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for comp in block.components:
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spec = maf_utilities.src_split(comp.src)[0]
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if spec not in species_found_in_maf:
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species_found_in_maf.append(spec)
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# indexed species
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for spec in indexed_for_species:
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if spec not in species_indexed_in_maf:
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print("Line %i, %s claims to be indexed for %s, but indexes do not exist." % (i, uid, spec))
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for spec in species_indexed_in_maf:
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if spec not in indexed_for_species:
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print("Line %i, %s is indexed for %s, but is not listed in loc file." % (i, uid, spec))
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# existing species
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for spec in species_exist:
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if spec not in species_found_in_maf:
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print("Line %i, %s claims to have blocks for %s, but was not found in MAF files." % (i, uid, spec))
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for spec in species_found_in_maf:
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if spec not in species_exist:
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print("Line %i, %s contains %s, but is not listed in loc file." % (i, uid, spec))
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except Exception as e:
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print("Line %i is invalid: %s" % (i, e))
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if __name__ == "__main__":
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__main__()
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