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