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comparison pair_fetch_DNA_ff.py @ 0:70f8259b0b30 draft

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author arkarachai-fungtammasan
date Wed, 01 Apr 2015 16:48:58 -0400
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-1:000000000000 0:70f8259b0b30
1 #!/usr/bin/env python
2 # pair_fetch_DNA_ff.py
3 # Function: filter microsat and flanking region by quality score;
4 # remove read with any base that has lower quality score than "quality_require" within "flanking_base" and convert from snoope to fastq
5 # Note that require flanking length need to be screen by Bob snoope script first
6
7 # Author: Arkarachai Fungtammasan
8 # Version 1.0.0 (15 July 2012)
9 # Input format: length_of_repeat[0] left_flank_length[1] right_flank_length[2] repeat_motif[3] hamming_distance[4] read_name[5] read_sequence[6] read_quality[7]
10 # Output format: two fastq file. First file contain left flank. Second file contain right flank.
11 # Command: python pair_fetch_DNA_ff.py input.txt
12
13 import sys
14 from galaxy import eggs
15
16 def stop_err(msg):
17 sys.stderr.write(msg)
18 sys.exit()
19
20 # read file name
21
22
23
24 filename=sys.argv[1]
25 L_filename=sys.argv[2]
26 R_filename=sys.argv[3]
27 quality_require=sys.argv[4]
28 flanking_base=sys.argv[5]
29 try:
30 quality_require=int(quality_require)
31 flanking_base=int(flanking_base)
32 except Exception, eee:
33 print eee
34 stop_err("Quality score cutoff and Length of flanking regions that require quality screening must be integer")
35
36 fd=open(filename)
37 fdd1=open(L_filename,'w')
38 fdd2=open(R_filename,'w')
39 lines=fd.xreadlines()
40 for line in lines:
41 temp=line.strip().split('\t')
42 temp=filter(None,temp)
43 #get index
44 left_flank=(0,int(temp[1]))
45 microsat=(int(temp[1]),int(temp[1])+int(temp[0]))
46 right_flank=(int(temp[1])+int(temp[0]),int(temp[1])+int(temp[0])+int(temp[2]))
47 flag=0
48 #filter length of left and right flank
49 if (right_flank[1]-right_flank[0])<flanking_base:
50 continue
51 if (left_flank[1]-left_flank[0])<flanking_base:
52 continue
53 #filter quality score
54 for i in temp[7][microsat[0]-flanking_base:microsat[1]+flanking_base]:
55 if ord(i)<(quality_require+33):
56 flag=1
57 else:
58 flag=flag
59 #print out to seperated files
60 if flag ==0:
61 newname= temp[5]##+'_'+temp[3]+'_'+temp[0]
62 fdd1.writelines('@'+newname+'\n')
63 fdd2.writelines('@'+newname+'\n')
64 fdd1.writelines(temp[6][left_flank[0]:left_flank[1]]+'\n')
65 fdd2.writelines(temp[6][right_flank[0]:right_flank[1]]+'\n')
66 fdd1.writelines('+'+newname+'\n')
67 fdd2.writelines('+'+newname+'\n')
68 fdd1.writelines(temp[7][left_flank[0]:left_flank[1]]+'\n')
69 fdd2.writelines(temp[7][right_flank[0]:right_flank[1]]+'\n')
70
71 fd.close()
72 fdd1.close()
73 fdd2.close()
74
75