annotate Iterative_mapping/iterative_map.py @ 87:5a9183ec344f draft

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1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3 
4 import sys
5 import os
6 from read_file import *
7 from read_s_file import *
8 import random
9 import string
10 
11 type_input = sys.argv[1]
12 seq_file = sys.argv[2]
13 ref_file = sys.argv[3]
14 shift = sys.argv[4]
15 length = sys.argv[5]
16 t_end = sys.argv[6]
17 map_type = sys.argv[7]
18 output_file = sys.argv[8]
19 
20 
21 if map_type!="default":
22     s = ""
23     sm = ""
24     s = s+"-v "+sys.argv[9]
25     sm = sm+"-v "+sys.argv[9]
26     sm = sm+" -5 "+sys.argv[10]
27     sm = sm+" -3 "+sys.argv[11]
28     s = s+" -k "+sys.argv[12]
29     sm = sm+" -k "+sys.argv[12]
30     if sys.argv[13]:
31         s = s+" -a"
32         sm = sm+" -a"
33     if int(sys.argv[14])>=1:
34         s = s+" -m "+sys.argv[14]
35         sm = sm+" -m "+sys.argv[14]
36     if sys.argv[15]:
37         s = s+" --best --strata "
38         sm = sm+" --best --strata "
39     
40 else:
41     s = "-v 3 -a --best --strata "
42     sm = "-v 3 -a --best --strata "
43 
44 ospath = os.path.realpath(sys.argv[0])
45 ost = ospath.split('/')
46 syspath = ""
47 for i in range(len(ost)-1):
48     syspath = syspath+ost[i].strip()
49     syspath = syspath+'/'
50 
51 syspathrs = os.getcwd()
52 syspathrs = syspathrs+'/'
53 
54 os.system("bowtie-build -f "+ref_file+" "+syspathrs+"ref > "+syspathrs+"log.txt")
55 
56 os.system("cp "+seq_file+" "+syspathrs+"seq0.fa")
57 
58 if type_input == "fasta":
59     tp = 'fasta'
60 if type_input == "fastq":
61     tp = 'fastq'
62 
63 k = 0
64 
65 if type_input == "fasta":
66     os.system("bowtie "+sm+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
67 if type_input == "fastq":
68     os.system("bowtie "+sm+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
69 
70 while(True):
71     os.system("samtools view -Sb -F 0xfff "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"mapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get mapped reads
72     os.system("samtools view -Sb -f 0x4 "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"umapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get unmapped reads
73     os.system("samtools view -Sb -f 0x10 "+syspathrs+"map"+str(k)+".sam > "+syspathrs+"rmapped"+str(k)+".bam 2>"+syspathrs+"log.txt") #get reversed mapped reads
74     os.system("samtools merge -f "+syspathrs+"unmapped"+str(k)+".bam "+syspathrs+"umapped"+str(k)+".bam "+syspathrs+"rmapped"+str(k)+".bam") #get reversed mapped reads
75     os.system("samtools view -h -o "+syspathrs+"unmapped"+str(k)+".sam "+syspathrs+"unmapped"+str(k)+".bam") #get reversed mapped reads
76     if k>0:
77         os.system("samtools view -h -o "+syspathrs+"mapped"+str(k)+".sam "+syspathrs+"mapped"+str(k)+".bam") #get reversed mapped reads
78         os.system("cut -f 1 "+syspathrs+"unmapped"+str(k)+".sam > "+syspathrs+"unmapped"+str(k)+".txt")
79         os.system("cut -f 1 "+syspathrs+"mapped"+str(k)+".sam > "+syspathrs+"mapped"+str(k)+".txt")
80         os.system("python "+syspath+"remove_map.py "+syspathrs+"unmapped"+str(k)+".txt "+syspathrs+"mapped"+str(k)+".txt "+syspathrs+"runmapped"+str(k)+".txt")
81         os.system("rm "+syspathrs+"mapped"+str(k)+".sam")
82         os.system("rm "+syspathrs+"mapped"+str(k)+".txt")
83         os.system("rm "+syspathrs+"unmapped"+str(k)+".txt")
84     else:
85         os.system("cut -f 1 "+syspathrs+"unmapped"+str(k)+".sam > "+syspathrs+"runmapped"+str(k)+".txt")
86     
87     os.system("rm "+syspathrs+"unmapped"+str(k)+".bam")
88     os.system("rm "+syspathrs+"umapped"+str(k)+".bam")
89     os.system("rm "+syspathrs+"rmapped"+str(k)+".bam")
90     os.system("python "+syspath+"seq_track.py "+syspathrs+"runmapped"+str(k)+".txt "+syspathrs+"seq"+str(k)+".fa "+syspathrs+"unmap_seq"+str(k)+".fa "+tp) #get unmapped sequence
91     os.system("python "+syspath+"truncate.py "+syspathrs+"unmap_seq"+str(k)+".fa "+shift+" "+syspathrs+"seq"+str(k+1)+".fa "+length+" "+t_end) #truncate unmapped sequence
92     os.system("rm "+syspathrs+"seq"+str(k)+".fa") #Remove sequences being mapped
93     os.system("rm "+syspathrs+"map"+str(k)+".sam") #Remove mapping file
94     os.system("rm "+syspathrs+"unmap_seq"+str(k)+".fa") #Remove unmapped sequnce
95     os.system("rm "+syspathrs+"runmapped"+str(k)+".txt")
96     os.system("rm "+syspathrs+"unmapped"+str(k)+".sam")
97     
98     os.system("wc -l "+syspathrs+"seq"+str(k+1)+".fa > "+syspathrs+"count"+str(k+1)+".txt")
99     c = read_sp_file(syspathrs+"count"+str(k+1)+".txt")
00     if c[0][0] == '0': #If no reads is in the sequence file, stop
01         os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
02         os.system("rm "+syspathrs+"seq"+str(k+1)+".fa")
03         break
04     os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
05     k = k+1
06     if type_input == "fasta":
07         os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
08     if type_input == "fastq":
09         os.system("bowtie "+s+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
10 
11 
12 ss = ""
13 for i in range(0,k+1):
14     ss = ss+" "+syspathrs+"mapped"+str(i)+".bam"
15 
16 
17 os.system("samtools merge -f "+syspathrs+"combine.bam"+" "+ss)
18 os.system("samtools sort "+syspathrs+"combine.bam sorted")
19 os.system("samtools view -b -h sorted.bam > " + output_file)
20 #print("samtools merge mapped_all.bam"+ss)
21 os.system("rm "+syspathrs+"mapped*.bam")
22 os.system("rm "+syspathrs+"combine.bam")
23 os.system("rm "+syspathrs+"sorted.bam")
24 os.system("rm "+syspathrs+"ref*")
25 #os.system("rm -r "+syspathrs)
26 
27