root/galaxy-central/tools/solid_tools/maq_cs_wrapper.py

#!/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__()