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87 lines
2.8 KiB
Python
87 lines
2.8 KiB
Python
#!/usr/bin/env python
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"""
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Read a maf and output intervals for specified list of species.
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"""
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import os
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import sys
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from bx.align import maf
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from galaxy.tools.util import maf_utilities
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def __main__():
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input_filename = sys.argv[1]
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output_filename = sys.argv[2]
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output_id = sys.argv[3]
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# where to store files that become additional output
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database_tmp_dir = sys.argv[4]
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primary_spec = sys.argv[5]
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species = sys.argv[6].split(",")
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all_species = sys.argv[7].split(",")
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partial = sys.argv[8]
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keep_gaps = sys.argv[9]
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out_files = {}
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if "None" in species:
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species = []
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if primary_spec not in species:
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species.append(primary_spec)
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if primary_spec not in all_species:
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all_species.append(primary_spec)
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all_species.sort()
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for spec in species:
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if spec == primary_spec:
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out_files[spec] = open(output_filename, "w+")
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else:
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out_files[spec] = open(
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os.path.join(database_tmp_dir, "primary_%s_%s_visible_interval_%s" % (output_id, spec, spec)), "w+"
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)
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out_files[spec].write("#chrom\tstart\tend\tstrand\tscore\tname\t%s\n" % ("\t".join(all_species)))
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num_species = len(all_species)
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file_in = open(input_filename)
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maf_reader = maf.Reader(file_in)
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for i, m in enumerate(maf_reader):
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for j, block in enumerate(maf_utilities.iter_blocks_split_by_species(m)):
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if len(block.components) < num_species and partial == "partial_disallowed":
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continue
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sequences = {}
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for c in block.components:
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spec, chrom = maf_utilities.src_split(c.src)
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if keep_gaps == "remove_gaps":
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sequences[spec] = c.text.replace("-", "")
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else:
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sequences[spec] = c.text
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sequences = "\t".join(sequences.get(_, "") for _ in all_species)
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for spec in species:
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c = block.get_component_by_src_start(spec)
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if c is not None:
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spec2, chrom = maf_utilities.src_split(c.src)
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assert spec2 == spec, Exception(
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"Species name inconsistancy found in component: %s != %s" % (spec, spec2)
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)
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out_files[spec].write(
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"%s\t%s\t%s\t%s\t%s\t%s\t%s\n"
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% (
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chrom,
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c.forward_strand_start,
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c.forward_strand_end,
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c.strand,
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m.score,
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"%s_%s_%s" % (spec, i, j),
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sequences,
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)
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)
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file_in.close()
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for file_out in out_files.values():
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file_out.close()
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if __name__ == "__main__":
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__main__()
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