ProbeSelect.py

#!/usr/bin/env python

'''



Copyright 2010 Wu Albert Cheng <albertwcheng@gmail.com>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

'''

#Exon Array Probe Selection
#Xing, Y., Kapur, K., and Wong, W.H. 2006. Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS ONE in press.
#For questions and comments, please contact yi-xing@uiowa.edu or whwong@stanford.edu

import re
import sys
import os
import getopt

data_dir=sys.argv[1]
os.cur_dir=data_dir
array_list=os.listdir(os.cur_dir)
n_array=len(array_list)
FileHandlers=[]
array_name=[]

write_to_dir='out'

#read command line options
opts=sys.argv[2:]
try:
    optlist,args=getopt.getopt(opts,'t:r:')
except getopt.GetoptError:
    print "Usage: ProbeSelect.py DATA_DIR -t [T/F] -r [T/F]"
    sys.exit(2)
for o,a in optlist:
    if o=="-t":
        trim_zero=a
    if o=="-r":
        run_r=a

for Array in array_list:
    array_name.append(Array[:-4])
    data_file=data_dir+'/'+Array
    data_ifile=open(data_file,"r")
    FileHandlers.append(data_ifile)

#read one line from all files
def readline_all(FileHandlers):
    n_file=len(FileHandlers)
    lines=[]
    for i in range(n_file):
        line=FileHandlers[i].readline()
        line=line[:-1]
        lines.append(line)
    return lines

current_transcript_cluster_id='-1'

#skip the first two lines
readline_all(FileHandlers)
readline_all(FileHandlers)

while(1):
    lines=readline_all(FileHandlers)

    line=lines[0]
    line_data=re.split('\t',line)

    #Stop at transcript clusters with only extended and full probes
    if line_data[0]=='#ExtendedTranscriptClusters':
        ofile.close()
        break
    
    transcript_cluster_id=line_data[0]
    probeset_id=line_data[1]
    probe_level=line_data[2]
    probe_id=line_data[3]
    probe_intensity=line_data[5]

    if (transcript_cluster_id!=current_transcript_cluster_id):
        if (current_transcript_cluster_id!='-1'):
            ofile.close()
        
        current_transcript_cluster_id=transcript_cluster_id
    
        ofile=open(write_to_dir+'/'+str(transcript_cluster_id)+'.txt','w')
        print "Processing "+str(transcript_cluster_id)+'...'
        ofile.write(transcript_cluster_id)
        for Array in array_list:
            ofile.write("\t"+Array)
        ofile.write("\n")
    ofile.write(str(probe_id)+"|"+str(probeset_id)+"|"+str(probe_level))


    for line in lines:
        line_data=re.split("\t",line)
        probe_intensity=line_data[5]

        if (trim_zero!='F'):
            if float(probe_intensity)<=0:
                probe_intensity=0
        ofile.write("\t"+str(probe_intensity))
    ofile.write("\n")

if (run_r!='F'):
    import rpy
    rpy.r.source("ProbeSelect.R")