113 lines
3.4 KiB
Plaintext
113 lines
3.4 KiB
Plaintext
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#!/usr/bin/python
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import optparse
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import os
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import sys
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probes = {}
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bp = {}
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cc = {}
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mf = {}
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def split_value(string):
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"""Splits a tab delimited value from affymetrix csv files"""
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string = string.strip()
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values = [x.strip() for x in string.split('///')]
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if len(values) == 1 and values[0] == '---':
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return []
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return values
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def split_subvalues(string):
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"""Splits a value into smaller components"""
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string = string.strip()
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values = [x.strip() for x in string.split('//')]
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if len(values) == 1 and values[0] == '--':
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return []
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return values
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def set_probes(probe, entrez):
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"""Set probe values for each entrez value."""
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for gene_id in split_value(entrez):
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if not probes.has_key(gene_id):
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probes[gene_id] = []
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probes[gene_id].append(probe.strip())
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def set_go(d, entrez, terms):
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genes = split_value(entrez)
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terms = split_value(terms)
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for gene in genes:
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if not d.has_key(gene):
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d[gene] = []
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for term in terms:
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d[gene].append(split_subvalues(term)[0])
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def parse_options():
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op = optparse.OptionParser()
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op.add_option('-b', '--biological-process', dest="bp",
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help="Output annotations in the biological process tree.",
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action="store_true", default=False)
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op.add_option('-c', '--cellular-component', dest="cc",
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help="Output annotations in the cellular component tree.",
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action="store_true", default=False)
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op.add_option('-d', '--output-dataset',
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help="Export as ftsv (Fluents dataset) file.")
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op.add_option('-m', '--molecular-function', dest="mf",
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help="Output annotations in the molecular function tree.",
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action="store_true", default=False)
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op.add_option('-u', '--unique-terms-only', dest="only_terms",
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help="Output only a list of all unique GO terms annotated to the genes",
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action="store_true", default=False)
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return op.parse_args()
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def read_file(options):
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fd = open('entrez-go-mapping.cccsv')
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for line in fd.readlines():
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values = line.split(':::')
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probeid = values[0]
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set_probes(probeid, values[1])
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if options.bp:
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set_go(bp, values[1], values[2])
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if options.cc:
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set_go(cc, values[1], values[3])
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if options.mf:
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set_go(mf, values[1], values[4])
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fd.close()
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if __name__ == '__main__':
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options, args = parse_options()
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read_file(options)
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if options.only_terms:
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s = set()
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for gene in args:
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if options.bp and bp.has_key(gene):
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for x in bp[gene]:
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s.add(x)
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if options.mf and bp.has_key(gene):
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for x in mf[gene]:
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s.add(x)
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if options.cc and bp.has_key(gene):
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for x in cc[gene]:
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s.add(x)
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for term in s:
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print "GO:%07d" % int(term)
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sys.exit(0)
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for gene in args:
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print gene,
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if options.bp and bp.has_key(gene):
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for x in bp[gene]:
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print "GO:%07d" % int(x),
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if options.cc and bp.has_key(gene):
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for x in cc[gene]:
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print "GO:%07d" % int(x),
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if options.mf and bp.has_key(gene):
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for x in mf[gene]:
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print "GO:%07d" % int(x),
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print
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