72 lines
1.9 KiB
Plaintext
72 lines
1.9 KiB
Plaintext
|
#!/usr/bin/python
|
||
|
|
|
||
|
|
import getopt
|
||
|
|
import os, os.path
|
||
|
|
import sys
|
||
|
|
|
||
|
|
OUTPUT_COLS = ["Probe_Id", "RefSeq_ID", "Unigene_ID", "Entrez_Gene_ID", "Accession", "Symbol", "Chromosome", "Definition"]
|
||
|
|
|
||
|
|
def print_help():
|
||
|
|
print "laydi-annot-illumina"
|
||
|
|
print
|
||
|
|
print "Usage: laydi-annot-illumina <illumina-annotation-file.txt>"
|
||
|
|
print
|
||
|
|
print "Description:"
|
||
|
|
print " Produce laydi annotation files from Illumina text annotation files"
|
||
|
|
print " Illumina files can be downloaded from:"
|
||
|
|
print " http://www.switchtoi.com/annotationfiles.ilmn"
|
||
|
|
print
|
||
|
|
|
||
|
|
def parse_cmdline():
|
||
|
|
short_opts = "h"
|
||
|
|
long_opts = ["help"]
|
||
|
|
options, params = getopt.getopt(sys.argv[1:], short_opts, long_opts)
|
||
|
|
|
||
|
|
for key, val in options:
|
||
|
|
if key in ["-h", "--help"]:
|
||
|
|
print_help()
|
||
|
|
sys.exit(0)
|
||
|
|
|
||
|
|
if len(params) != 1:
|
||
|
|
print_help()
|
||
|
|
sys.exit(1)
|
||
|
|
|
||
|
|
return params[0]
|
||
|
|
|
||
|
|
def convert_annotations(fn_in, fn_out):
|
||
|
|
fd_in = open(fn_in)
|
||
|
|
fd_out = open(fn_out, "w")
|
||
|
|
|
||
|
|
# Skip headers
|
||
|
|
line = fd_in.readline()
|
||
|
|
while not line.startswith("[Probes]"):
|
||
|
|
line = fd_in.readline()
|
||
|
|
|
||
|
|
colnames = fd_in.readline().split("\t")
|
||
|
|
export_colnums = [colnames.index(x) for x in OUTPUT_COLS]
|
||
|
|
|
||
|
|
# Print output column headers
|
||
|
|
export_colnames = ["probe-id"] + colnames[1:]
|
||
|
|
print >> fd_out, "\t".join(export_colnames)
|
||
|
|
|
||
|
|
line = fd_in.readline()
|
||
|
|
while not line == "" and not line.startswith("["):
|
||
|
|
values = line.split("\t")
|
||
|
|
output_values = [values[x] for x in export_colnums]
|
||
|
|
print >> fd_out, "\t".join(output_values)
|
||
|
|
line = fd_in.readline()
|
||
|
|
|
||
|
|
if __name__ == "__main__":
|
||
|
|
fn_in = parse_cmdline()
|
||
|
|
fn_out = os.path.split(fn_in)[1]
|
||
|
|
fn_out = os.path.splitext(fn_out)[0] + ".annot"
|
||
|
|
|
||
|
|
print "Reading: %s" % (fn_in,)
|
||
|
|
print "Writing: %s" % (fn_out,)
|
||
|
|
print
|
||
|
|
print "Annotations:"
|
||
|
|
print ", ".join(OUTPUT_COLS)
|
||
|
|
|
||
|
|
convert_annotations(fn_in, fn_out)
|
||
|
|
|