94 lines
2.3 KiB
Plaintext
94 lines
2.3 KiB
Plaintext
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#!/usr/bin/python
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import getopt
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import os, os.path
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import sys
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OUTPUT_COLS = ["Array_Address_Id", "Entrez_Gene_ID", "Accession", "ILMN_Gene", "Definition", ]
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def print_help():
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print "laydi-mapping-illumina"
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print
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print "Usage: laydi-mapping-illumina <illumina-annotation-file.txt> <from_dim> <to_dim>"
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print
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print "Description:"
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print " Produce mapping files from Illumina text annotation files"
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print " Illumina files can be downloaded from:"
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print " http://www.switchtoi.com/annotationfiles.ilmn"
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print
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print " NOTE: <from_dim> and <to_dim> are the column names in the illumina text file,"
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print " not laydi dimensions."
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print
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def parse_cmdline():
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short_opts = "h"
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long_opts = ["help"]
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options, params = getopt.getopt(sys.argv[1:], short_opts, long_opts)
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for key, val in options:
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if key in ["-h", "--help"]:
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print_help()
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sys.exit(0)
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if len(params) != 3:
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print_help()
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sys.exit(1)
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return params
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def build_map(fn, from_dim, to_dim):
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retval = {}
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fd = open(fn)
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line = fd.readline()
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while line != "" and line.strip() != "[Probes]":
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line = fd.readline()
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if line == "":
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return None
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line = fd.readline()
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cols = [x.strip() for x in line.split("\t")]
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from_col = cols.index(from_dim)
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to_col = cols.index(to_dim)
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line = fd.readline()
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while line != "" and not line.strip().startswith("["):
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key = line.split("\t")[from_col]
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val = line.split("\t")[to_col]
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if not retval.has_key(key):
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retval[key] = [val]
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else:
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retval[key].append(val)
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line = fd.readline()
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return retval
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def write_map(fd, d, from_dim, to_dim):
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opened_here = False
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if isinstance(fd, str):
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fd = open(fd, "w")
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opened_here = True
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print >> fd, "# from: %s" % from_dim
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print >> fd, "# to: %s" % to_dim
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print >> fd, "# description: "
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print >> fd
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for k, v in d.items():
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print >> fd, k,
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for e in v:
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print >> fd, e,
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print >> fd
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if opened_here:
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fd.close()
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if __name__ == '__main__':
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fn, from_dim, to_dim = parse_cmdline()
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m = build_map(fn, from_dim, to_dim)
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write_map(sys.stdout, m, from_dim, to_dim)
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