--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/piq_wrapper.py	Wed May 24 00:36:16 2017 -0400
@@ -0,0 +1,155 @@
+#!/usr/bin/python
+
+import optparse, os, re, shutil, sys, tempfile, glob, shlex, vcf, pysam, tarfile, csv, operator
+from subprocess import *
+import subprocess
+import multiprocessing
+from joblib import Parallel, delayed
+from itertools import izip
+
+NCPU = multiprocessing.cpu_count()
+CHUNK_SIZE = 2**20 #1mb
+
+def create_dict(files):
+    tmp=dict()
+    t1 = [os.path.basename(i) for i in files]
+    t2 = ['-'.join(i.split('-')[0:2]) for i in t1 if 'RC' not in i]
+    for i in t2:
+        for j in files:
+            if i in j and i in tmp:
+                tmp[i].append(j)
+            elif i in j and i not in tmp:
+                tmp[i] = [j]
+            else:
+                continue
+    return tmp
+
+def file_merge(file1, file2, out_dir):
+    listF = (file1, file2)
+    outF=os.path.splitext(os.path.basename(file1))[0]
+    outExt = os.path.splitext(os.path.basename(file1))[1]
+    with open("%s/%s_merged%s" % (out_dir,outF,outExt),"wb") as fw:
+        for i in range(len(listF)):
+            with open(listF[i],"rb") as f:
+                writer = csv.writer(fw, delimiter=',', quotechar='', quoting=csv.QUOTE_NONE, escapechar='\\')
+                for i in range(len(listF)):
+                    with open(listF[i],"rb") as f:
+                        file_f=csv.reader(f, delimiter='\t')
+                        file_f.next()
+                        for line in file_f:
+                            writer.writerow(line)
+
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+def parallel_jobs(i, piq_dir_path, tmp_dir, inputF, out_dir, output_dir):
+    cmd=[]
+    motif=i
+    piq_cmd1 = "Rscript %s/pwmmatch.exact.r %s/common.r %s/jasparVertebrateCore2016-519-matrices.txt %d %s/; " % (piq_dir_path, piq_dir_path, piq_dir_path, motif, tmp_dir)
+    #piq_cmd1 = "Rscript %s/pwmmatch.exact.r %s/common.r %s/jasparfix.txt %d %s/; " % (piq_dir_path, piq_dir_path, piq_dir_path, motif, tmp_dir)
+    piq_cmd2 = "Rscript %s/bam2rdata.r %s/common.r %s/bam.RData %s; " % (piq_dir_path, piq_dir_path, tmp_dir, inputF)
+    piq_cmd3 = "Rscript %s/pertf.r %s/common.r %s/ %s %s/ %s/bam.RData %d; "  % (piq_dir_path, piq_dir_path, tmp_dir, tmp_dir, out_dir, tmp_dir, motif)
+    piq_cmd = piq_cmd1+piq_cmd2+piq_cmd3
+    cmd.append(piq_cmd)
+    cmd="".join(cmd)
+    #print "cmd:%s" % cmd
+    stdout = tempfile.NamedTemporaryFile( prefix="piq-stdout-", dir=tmp_dir )
+    stderr = tempfile.NamedTemporaryFile( prefix="piq-stderr-", dir=tmp_dir )
+    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=output_dir )
+    return_code = proc.wait()
+
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+        stderr.flush()
+        stderr.seek(0)
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    stdout.close()
+    
+def __main__():
+    piq_dir_path="/mnt/galaxyTools/tools/piq/1.3/thashim"
+    parser = optparse.OptionParser()
+    parser.add_option('', '--input', dest="inputF", action='store', type="string", default=None, help='')
+    parser.add_option( '', '--output', dest='outputF', action='store', type="string", default=None, help='')
+    parser.add_option( '', '--out-dir', dest='output_dir', action='store', type="string", default=None, help='If specified, the output directory for extra files.' )
+
+    (options, args) = parser.parse_args()
+
+    if not os.path.exists(options.output_dir): 
+        os.mkdir(options.output_dir)
+    out_dir = "%s/out" % options.output_dir; 
+    if not os.path.exists(out_dir):
+        os.mkdir(out_dir)
+    tmp_dir = "%s/tmp" % options.output_dir; 
+    if not os.path.exists(tmp_dir):
+        os.mkdir(tmp_dir)
+
+    maxMotif=519
+    Parallel(n_jobs=NCPU)(delayed(parallel_jobs)(i, piq_dir_path, tmp_dir, options.inputF, out_dir, options.output_dir) for i in range(1,maxMotif+1))
+    
+    #combine files
+    csvFiles =sorted(glob.glob("%s/*calls.all.csv" % out_dir))
+    csvList=create_dict(csvFiles) 
+    
+    for v in csvList.values():
+        if len(v) == 2:
+            file_merge(v[0],v[1],out_dir)
+        else:
+            outF=os.path.splitext(os.path.basename(v[0]))[0]
+            outExt=os.path.splitext(os.path.basename(v[0]))[1]
+            shutil.copy(v[0],"%s/%s_merged%s" % (out_dir, outF, outExt))
+
+    bedFiles=sorted(glob.glob("%s/*calls.all.bed" % out_dir))
+    bedList=create_dict(bedFiles)
+
+    for v in bedList.values():
+        if len(v) == 2:
+            file_merge(v[0],v[1],out_dir)
+        else:
+            outF=os.path.splitext(os.path.basename(v[0]))[0]
+            outExt=os.path.splitext(os.path.basename(v[0]))[1]
+            shutil.copy(v[0],"%s/%s_merged%s" % (out_dir, outF, outExt))
+
+    m_csvFiles=sorted(glob.glob("%s/*_merged.csv" % out_dir))
+    m_bedFiles=sorted(glob.glob("%s/*_merged.bed" % out_dir))
+
+    for i in range(len(m_csvFiles)):
+        outF=os.path.splitext(os.path.basename(m_csvFiles[i]))[0]
+        #print "\noutF: %s\n" % outF
+        with open('%s/%s_all_tmp' % (out_dir,outF), 'wb') as res, open(m_bedFiles[i]) as f1, open(m_csvFiles[i]) as f2:
+            for line1, line2 in zip(f1, f2):
+                res.write("{},{}\n".format(line1.rstrip(), line2.rstrip()))
+        with open('%s/%s_all_tmp' % (out_dir,outF), "rb") as f3:
+            rdr=csv.reader(f3)
+
+            with open('%s/%s_final.bed' % (out_dir,outF),'wb') as result:
+                wtr = csv.writer(result, delimiter='\t', quotechar='', quoting=csv.QUOTE_NONE)
+                #for r in sorted_list:
+                for r in rdr:
+                    if len(r) > 12:
+                        wtr.writerow((r[0],r[1],r[2],r[3],r[5],r[9].replace('\\',""),r[10].replace('\\',""),r[11].replace('\\',""),r[12]))
+    filenames=sorted(glob.glob("%s/*_final.bed" % out_dir))
+    #shutil.copy('%s/*_final.bed' % out_dir, options.output_dir)
+    with open('%s/all_motif_comb_final.bed' % options.output_dir, 'w') as outfile:
+        for fname in filenames:
+            shutil.copy('%s' % fname, options.output_dir)
+            with open(fname) as infile:
+                for line in infile:
+                    outfile.write(line)
+
+    shutil.copy('%s/all_motif_comb_final.bed' % options.output_dir, options.outputF)
+
+    # concatenerate calls.all and RC.calls.all for csv and bed files
+    cleanup_before_exit( options.output_dir )
+
+if __name__=="__main__": __main__()
+