diff tools/solid_tools/maq_cs_wrapper.py @ 0:9071e359b9a3

Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/solid_tools/maq_cs_wrapper.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,270 @@
+#!/usr/bin/env python
+#Guruprasad Ananda
+#MAQ mapper for SOLiD colourspace-reads
+
+import sys, os, zipfile, tempfile, subprocess
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+ 
+def __main__():
+
+    out_fname = sys.argv[1].strip()
+    out_f2 = open(sys.argv[2].strip(),'r+')
+    ref_fname = sys.argv[3].strip()
+    f3_read_fname = sys.argv[4].strip()
+    f3_qual_fname = sys.argv[5].strip()
+    paired = sys.argv[6]
+    if paired == 'yes':
+        r3_read_fname = sys.argv[7].strip()
+        r3_qual_fname = sys.argv[8].strip()
+    min_mapqual = int(sys.argv[9].strip())
+    max_mismatch = int(sys.argv[10].strip())
+    out_f3name = sys.argv[11].strip()   
+    subprocess_dict = {}
+
+    ref_csfa = tempfile.NamedTemporaryFile()
+    ref_bfa = tempfile.NamedTemporaryFile()
+    ref_csbfa = tempfile.NamedTemporaryFile()
+    cmd2_1 = 'maq fasta2csfa %s > %s 2>&1' %(ref_fname,ref_csfa.name)
+    cmd2_2 = 'maq fasta2bfa %s %s 2>&1' %(ref_csfa.name,ref_csbfa.name)
+    cmd2_3 = 'maq fasta2bfa %s %s 2>&1' %(ref_fname,ref_bfa.name)
+    try:
+        os.system(cmd2_1)
+        os.system(cmd2_2)
+        os.system(cmd2_3)
+    except Exception, erf:
+        stop_err(str(erf)+"Error processing reference sequence")
+        
+    if paired == 'yes': #paired end reads
+        tmpf = tempfile.NamedTemporaryFile()    #forward reads
+        tmpr = tempfile.NamedTemporaryFile()    #reverse reads
+        tmps = tempfile.NamedTemporaryFile()    #single reads
+        tmpffastq = tempfile.NamedTemporaryFile()
+        tmprfastq = tempfile.NamedTemporaryFile()
+        tmpsfastq = tempfile.NamedTemporaryFile()
+
+        cmd1 = "solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,tmps.name,f3_read_fname,f3_qual_fname,r3_read_fname,r3_qual_fname)
+        try:
+            os.system(cmd1)
+            os.system('gunzip -c %s >> %s' %(tmpf.name,tmpffastq.name))
+            os.system('gunzip -c %s >> %s' %(tmpr.name,tmprfastq.name))
+            os.system('gunzip -c %s >> %s' %(tmps.name,tmpsfastq.name))
+
+        except Exception, eq:
+            stop_err("Error converting data to fastq format." + str(eq))
+        
+        #make a temp directory where the split fastq files will be stored
+        try: 
+            split_dir = tempfile.mkdtemp()
+            split_file_prefix_f = tempfile.mktemp(dir=split_dir)
+            split_file_prefix_r = tempfile.mktemp(dir=split_dir)
+            splitcmd_f = 'split -a 2 -l %d %s %s' %(32000000,tmpffastq.name,split_file_prefix_f) #32M lines correspond to 8M reads
+            splitcmd_r = 'split -a 2 -l %d %s %s' %(32000000,tmprfastq.name,split_file_prefix_r) #32M lines correspond to 8M reads
+
+            os.system(splitcmd_f)
+            os.system(splitcmd_r)
+            os.chdir(split_dir)
+            ii = 0
+            for fastq in os.listdir(split_dir):
+                if not fastq.startswith(split_file_prefix_f.split("/")[-1]):
+                    continue
+                fastq_r = split_file_prefix_r + fastq.split(split_file_prefix_f.split("/")[-1])[1] #find the reverse strand fastq corresponding to formward strand fastq
+                tmpbfq_f = tempfile.NamedTemporaryFile()
+                tmpbfq_r = tempfile.NamedTemporaryFile()
+                cmd3 = 'maq fastq2bfq %s %s 2>&1; maq fastq2bfq %s %s 2>&1; maq map -c %s.csmap %s %s %s 1>/dev/null 2>&1; maq mapview %s.csmap > %s.txt' %(fastq,tmpbfq_f.name,fastq_r,tmpbfq_r.name,fastq,ref_csbfa.name,tmpbfq_f.name,tmpbfq_r.name,fastq,fastq)
+                subprocess_dict['sp'+str(ii+1)] = subprocess.Popen([cmd3],shell=True,stdout=subprocess.PIPE)
+                ii += 1
+            while True:
+                all_done = True
+                for j,k in enumerate(subprocess_dict.keys()):
+                    if subprocess_dict['sp'+str(j+1)].wait() != 0:
+                        err = subprocess_dict['sp'+str(j+1)].communicate()[1] 
+                        if err != None:
+                            stop_err("Mapping error: %s" %err)
+                        all_done = False
+                if all_done:
+                    break
+            cmdout = "for map in *.txt; do cat $map >> %s; done" %(out_fname)
+            os.system(cmdout)
+            
+            tmpcsmap = tempfile.NamedTemporaryFile()
+            cmd_cat_csmap = "for csmap in *.csmap; do cat $csmap >> %s; done" %(tmpcsmap.name)
+            os.system(cmd_cat_csmap)
+            
+            tmppileup = tempfile.NamedTemporaryFile()
+            cmdpileup = "maq pileup -m %s -q %s %s %s > %s" %(max_mismatch,min_mapqual,ref_bfa.name,tmpcsmap.name,tmppileup.name)
+            os.system(cmdpileup)
+            tmppileup.seek(0)
+            print >> out_f2, "#chr\tposition\tref_nt\tcoverage\tSNP_count\tA_count\tT_count\tG_count\tC_count"
+            for line in file(tmppileup.name):
+                elems = line.strip().split()
+                ref_nt = elems[2].capitalize()
+                read_nt = elems[4]
+                coverage = int(elems[3])
+                a,t,g,c = 0,0,0,0
+                ref_nt_count = 0
+                for ch in read_nt:
+                    ch = ch.capitalize()
+                    if ch not in ['A','T','G','C',',','.']:
+                        continue
+                    if ch in [',','.']:
+                        ch = ref_nt
+                        ref_nt_count += 1
+                    try:
+                        nt_ind = ['A','T','G','C'].index(ch)
+                        if nt_ind == 0:
+                            a+=1
+                        elif nt_ind == 1:
+                            t+=1
+                        elif nt_ind == 2:
+                            g+=1
+                        else:
+                            c+=1
+                    except ValueError, we:
+                        print >>sys.stderr, we
+                print >> out_f2, "%s\t%s\t%s\t%s\t%s\t%s" %("\t".join(elems[:4]),coverage-ref_nt_count,a,t,g,c)
+        except Exception, er2:
+            stop_err("Encountered error while mapping: %s" %(str(er2)))
+            
+    
+    else:   #single end reads
+        tmpf = tempfile.NamedTemporaryFile()   
+        tmpfastq = tempfile.NamedTemporaryFile()
+        cmd1 = "solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,None,None,f3_read_fname,f3_qual_fname,None,None)
+        try:
+            os.system(cmd1)
+            os.system('gunzip -c %s >> %s' %(tmpf.name,tmpfastq.name))
+            tmpf.close()
+        except:
+            stop_err("Error converting data to fastq format.")
+        
+        #make a temp directory where the split fastq files will be stored
+        try: 
+            split_dir = tempfile.mkdtemp()
+            split_file_prefix = tempfile.mktemp(dir=split_dir)
+            splitcmd = 'split -a 2 -l %d %s %s' %(32000000,tmpfastq.name,split_file_prefix) #32M lines correspond to 8M reads
+            os.system(splitcmd)
+            os.chdir(split_dir)
+            for i,fastq in enumerate(os.listdir(split_dir)):
+                tmpbfq = tempfile.NamedTemporaryFile()
+                cmd3 = 'maq fastq2bfq %s %s 2>&1; maq map -c %s.csmap %s %s  1>/dev/null 2>&1; maq mapview %s.csmap > %s.txt' %(fastq,tmpbfq.name,fastq,ref_csbfa.name,tmpbfq.name,fastq,fastq)
+                subprocess_dict['sp'+str(i+1)] = subprocess.Popen([cmd3],shell=True,stdout=subprocess.PIPE)
+            
+            while True:
+                all_done = True
+                for j,k in enumerate(subprocess_dict.keys()):
+                    if subprocess_dict['sp'+str(j+1)].wait() != 0:
+                        err = subprocess_dict['sp'+str(j+1)].communicate()[1] 
+                        if err != None:
+                            stop_err("Mapping error: %s" %err)
+                        all_done = False
+                if all_done:
+                    break
+
+            cmdout = "for map in *.txt; do cat $map >> %s; done" %(out_fname)
+            os.system(cmdout)
+            
+            tmpcsmap = tempfile.NamedTemporaryFile()
+            cmd_cat_csmap = "for csmap in *.csmap; do cat $csmap >> %s; done" %(tmpcsmap.name)
+            os.system(cmd_cat_csmap)
+            
+            tmppileup = tempfile.NamedTemporaryFile()
+            cmdpileup = "maq pileup -m %s -q %s %s %s > %s" %(max_mismatch,min_mapqual,ref_bfa.name,tmpcsmap.name,tmppileup.name)
+            os.system(cmdpileup)
+            tmppileup.seek(0)
+            print >> out_f2, "#chr\tposition\tref_nt\tcoverage\tSNP_count\tA_count\tT_count\tG_count\tC_count"
+            for line in file(tmppileup.name):
+                elems = line.strip().split()
+                ref_nt = elems[2].capitalize()
+                read_nt = elems[4]
+                coverage = int(elems[3])
+                a,t,g,c = 0,0,0,0
+                ref_nt_count = 0
+                for ch in read_nt:
+                    ch = ch.capitalize()
+                    if ch not in ['A','T','G','C',',','.']:
+                        continue
+                    if ch in [',','.']:
+                        ch = ref_nt
+                        ref_nt_count += 1
+                    try:
+                        nt_ind = ['A','T','G','C'].index(ch)
+                        if nt_ind == 0:
+                            a+=1
+                        elif nt_ind == 1:
+                            t+=1
+                        elif nt_ind == 2:
+                            g+=1
+                        else:
+                            c+=1
+                    except:
+                        pass
+                print >> out_f2, "%s\t%s\t%s\t%s\t%s\t%s" %("\t".join(elems[:4]),coverage-ref_nt_count,a,t,g,c)
+        except Exception, er2:
+            stop_err("Encountered error while mapping: %s" %(str(er2)))
+    
+    #Build custom track from pileup
+    chr_list=[]
+    out_f2.seek(0)
+    fcov = tempfile.NamedTemporaryFile()
+    fout_a = tempfile.NamedTemporaryFile()
+    fout_t = tempfile.NamedTemporaryFile()
+    fout_g = tempfile.NamedTemporaryFile()
+    fout_c = tempfile.NamedTemporaryFile()
+    fcov.write('''track type=wiggle_0 name="Coverage track" description="Coverage track (from Galaxy)" color=0,0,0 visibility=2\n''')
+    fout_a.write('''track type=wiggle_0 name="Track A" description="Track A (from Galaxy)" color=255,0,0 visibility=2\n''')
+    fout_t.write('''track type=wiggle_0 name="Track T" description="Track T (from Galaxy)" color=0,255,0 visibility=2\n''')
+    fout_g.write('''track type=wiggle_0 name="Track G" description="Track G (from Galaxy)" color=0,0,255 visibility=2\n''')
+    fout_c.write('''track type=wiggle_0 name="Track C" description="Track C (from Galaxy)" color=255,0,255 visibility=2\n''')
+    
+    for line in out_f2:
+        if line.startswith("#"):
+            continue
+        elems = line.split()
+        chr = elems[0]
+            
+        if chr not in chr_list:
+            chr_list.append(chr)
+            if not (chr.startswith('chr') or chr.startswith('scaffold')):
+                chr = 'chr'
+            header = "variableStep chrom=%s" %(chr)
+            fcov.write("%s\n" %(header))
+            fout_a.write("%s\n" %(header))
+            fout_t.write("%s\n" %(header))
+            fout_g.write("%s\n" %(header))
+            fout_c.write("%s\n" %(header))
+        try:
+            pos = int(elems[1])
+            cov = int(elems[3])
+            a = int(elems[5])
+            t = int(elems[6])
+            g = int(elems[7])
+            c = int(elems[8])
+        except:
+            continue
+        fcov.write("%s\t%s\n" %(pos,cov))
+        try:
+            a_freq = a*100./cov
+            t_freq = t*100./cov
+            g_freq = g*100./cov
+            c_freq = c*100./cov
+        except ZeroDivisionError:
+            a_freq=t_freq=g_freq=c_freq=0
+        fout_a.write("%s\t%s\n" %(pos,a_freq))
+        fout_t.write("%s\t%s\n" %(pos,t_freq))
+        fout_g.write("%s\t%s\n" %(pos,g_freq))
+        fout_c.write("%s\t%s\n" %(pos,c_freq))
+
+    fcov.seek(0)
+    fout_a.seek(0)
+    fout_g.seek(0)
+    fout_t.seek(0)
+    fout_c.seek(0)
+    os.system("cat %s %s %s %s %s | cat > %s" %(fcov.name,fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_f3name))
+
+if __name__=="__main__":
+    __main__()
+        
+