73 lines
2.1 KiB
Python
Executable File
73 lines
2.1 KiB
Python
Executable File
#!/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", "Chromosome", "Definition", "Ontology_Component", "Ontology_Process", "Ontology_Function", "ILMN_Gene"]
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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-annot-illumina"
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print
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print "Usage: laydi-annot-illumina <illumina-annotation-file.txt>"
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print
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print "Description:"
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print " Produce laydi annotation 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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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) != 1:
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print_help()
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sys.exit(1)
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return params[0]
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def convert_annotations(fn_in, fn_out):
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fd_in = open(fn_in)
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fd_out = open(fn_out, "w")
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# Skip headers
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line = fd_in.readline()
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while not line.startswith("[Probes]"):
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line = fd_in.readline()
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colnames = fd_in.readline().split("\t")
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export_colnums = [colnames.index(x) for x in OUTPUT_COLS]
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# Print output column headers
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export_colnames = ["probe-id"] + OUTPUT_COLS[1:]
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print >> fd_out, "\t".join(OUTPUT_COLS)
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line = fd_in.readline()
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while not line == "" and not line.startswith("["):
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values = line.split("\t")
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output_values = [values[x] for x in export_colnums]
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print >> fd_out, "\t".join(output_values)
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line = fd_in.readline()
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if __name__ == "__main__":
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fn_in = parse_cmdline()
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fn_out = os.path.split(fn_in)[1]
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fn_out = os.path.splitext(fn_out)[0] + ".annot"
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print "Reading: %s" % (fn_in,)
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print "Writing: %s" % (fn_out,)
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print
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print "Annotations:"
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print ", ".join(OUTPUT_COLS)
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convert_annotations(fn_in, fn_out)
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