# HG changeset patch
# User malex
# Date 1322673535 18000
# Node ID 2a3c8b2d597934ede231b58c0f4304edfc989a4e
# Parent  7676570eb676bd458834c070094a9aa2a340f5dd
Uploaded the wrapper file

diff -r 7676570eb676 -r 2a3c8b2d5979 trf_wrapper.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trf_wrapper.py	Wed Nov 30 12:18:55 2011 -0500
@@ -0,0 +1,122 @@
+#!/usr/bin/env python
+
+"""
+Runs TRF on a sequence file.
+For use with trf version 4.04
+
+usage: trf_wrapper.py input_file <required parameters> [options]
+     Required parameters:
+    match
+    mismatch
+    indels
+    match_probability (%, 10-100)
+    indel_probability (%, 10-100)
+    minimal score (30-150)
+    maximum period size (1-2000)
+"""
+
+import optparse, os, shutil, subprocess, sys, re
+from os.path import abspath
+
+def remove_bgcolor(infilename,outfilename):
+    infile = open(infilename, "r")
+    outfile = open(outfilename, "w")
+    bgcolor = re.compile(r'FBF8BC')
+    for line in infile:
+        line = bgcolor.sub('FFFFFF', line)
+        outfile.write(line)
+    infile.close()
+    outfile.close()
+    os.remove(infilename)
+
+def remove_html(infilename,outfilename):
+    infile = open(infilename, "r")
+    outfile = open(outfilename, "w")
+    opena = re.compile(r'<A\ HREF.*?>')
+    bgcolor = re.compile(r'FBF8BC')
+    closea = re.compile(r'</A>')
+    for line in infile:
+        line = opena.sub('', line)
+        line = bgcolor.sub('FFFFFF', line)
+        line = closea.sub('', line)
+        outfile.write(line)
+    infile.close()
+    outfile.close()
+    os.remove(infilename)
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
+
+def __main__():
+    #Parse arguments
+    usage = "usage: %prog input match mismatch indels match_p indel_p min_score max_period [options]"
+    parser = optparse.OptionParser(usage)
+    parser.add_option( '-f', '--flanking', dest='flanking', action='store_true', help='Flanking sequence' )
+    parser.add_option( '-m', '--masked', dest='masked', action='store_true', help='Masked sequence' )
+    parser.add_option( '-r', '--redundancy', dest='redundancy', action='store_true', help='No redundance elimination' )
+    parser.add_option( '-o', '--datoutput', dest='datoutput', action='store', help='Output data file name' )
+    parser.add_option( '-k', '--maskoutput', dest='maskoutput', action='store', help='Output mask file name' )
+    parser.add_option( '-t', '--report', dest='report', action='store', help='Report file name' )
+    parser.add_option( '-i', '--indices', dest='indices', action='store', help='Indices file name' )
+    (opts, arguments) = parser.parse_args()
+
+    # Arguments and options
+    if len(arguments) != 8:
+        print(usage)
+        stop_err('Wrong number of arguments passed')
+    output_dat = "%s.%s.%s.%s.%s.%s.%s.%s.dat" % (tuple(arguments))
+    output_mask = "%s.%s.%s.%s.%s.%s.%s.%s.mask" % (tuple(arguments))
+    output_report = "%s.%s.%s.%s.%s.%s.%s.%s.1.html" % (tuple(arguments))
+    output_indices = "%s.%s.%s.%s.%s.%s.%s.%s.1.txt.html" % (tuple(arguments))
+
+    if opts.masked and opts.masked == True:
+        arguments.append('-m')
+    if opts.flanking and opts.flanking == True:
+        arguments.append('-f')
+    if opts.redundancy and opts.redundancy  == True:
+        arguments.append('-r')
+    if opts.datoutput and opts.datoutput  != '':
+        output_dat_filename = opts.datoutput
+    if opts.maskoutput and opts.maskoutput  != '':
+        output_mask_filename = opts.maskoutput
+    if opts.report and opts.report  != '':
+        output_report_filename = opts.report
+    if opts.indices and opts.indices  != '':
+        output_indices_filename = opts.indices
+
+    # Run
+    cmd = arguments
+    cmd.insert(0,"trf")
+    # Produce both html and dat files
+    cmd.append("-d")
+    try:
+        proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except Exception, err:
+        sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
+        sys.exit(1)
+    stdout, stderr = proc.communicate()
+    return_code = proc.returncode
+    if return_code != 1:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+        sys.stderr.write("%s\n" % cmd)
+    else:
+        sys.stdout.write(stdout)
+        sys.stdout.write(stderr)
+    cdir = os.getcwd()
+    file_list = os.listdir(cdir)
+    try:
+        report_file = os.path.basename(output_report)
+        indices_file = os.path.basename(output_indices)
+        remove_html(report_file, output_report_filename)
+        remove_bgcolor(indices_file, output_indices_filename)
+        shutil.move(os.path.basename(output_dat), output_dat_filename)
+#        shutil.copyfile(os.path.basename(output_report), output_report_filename)
+#        shutil.copyfile(os.path.basename(output_indices), output_indices_filename)
+        if opts.masked and opts.masked == True:
+            shutil.move(os.path.basename(output_mask), output_mask_filename)
+    except Exception, err:
+        sys.stderr.write("Error copying output files: \n%s\n" % err)
+if __name__=="__main__": __main__()