Mercurial > repos > devteam > mapping_to_ucsc

comparison mapping_to_ucsc.py @ 0:601abbd22cea draft

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Imported from capsule None
author devteam
date Mon, 19 May 2014 12:33:55 -0400
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-1:000000000000 0:601abbd22cea
1 #!/usr/bin/env python
2
3 import sys, tempfile, os
4
5 assert sys.version_info[:2] >= (2.4)
6
7 def stop_err(msg):
8 sys.stderr.write(msg)
9 sys.exit()
10
11 def main():
12
13 out_fname = sys.argv[1]
14 in_fname = sys.argv[2]
15 chr_col = int(sys.argv[3])-1
16 coord_col = int(sys.argv[4])-1
17 track_type = sys.argv[5]
18 if track_type == 'coverage' or track_type == 'both':
19 coverage_col = int(sys.argv[6])-1
20 cname = sys.argv[7]
21 cdescription = sys.argv[8]
22 ccolor = sys.argv[9].replace('-',',')
23 cvisibility = sys.argv[10]
24 if track_type == 'snp' or track_type == 'both':
25 if track_type == 'both':
26 j = 5
27 else:
28 j = 0
29 #sname = sys.argv[7+j]
30 sdescription = sys.argv[6+j]
31 svisibility = sys.argv[7+j]
32 #ref_col = int(sys.argv[10+j])-1
33 read_col = int(sys.argv[8+j])-1
34
35
36 # Sort the input file based on chromosome (alphabetically) and start co-ordinates (numerically)
37 sorted_infile = tempfile.NamedTemporaryFile()
38 try:
39 os.system("sort -k %d,%d -k %dn -o %s %s" %(chr_col+1,chr_col+1,coord_col+1,sorted_infile.name,in_fname))
40 except Exception, exc:
41 stop_err( 'Initialization error -> %s' %str(exc) )
42
43 #generate chr list
44 sorted_infile.seek(0)
45 chr_vals = []
46 for line in file( sorted_infile.name ):
47 line = line.strip()
48 if not(line):
49 continue
50 try:
51 fields = line.split('\t')
52 chr = fields[chr_col]
53 if chr not in chr_vals:
54 chr_vals.append(chr)
55 except:
56 pass
57 if not(chr_vals):
58 stop_err("Skipped all lines as invalid.")
59
60 if track_type == 'coverage' or track_type == 'both':
61 if track_type == 'coverage':
62 fout = open( out_fname, "w" )
63 else:
64 fout = tempfile.NamedTemporaryFile()
65 fout.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
66 % ( cname, cdescription, ccolor, cvisibility ))
67 if track_type == 'snp' or track_type == 'both':
68 fout_a = tempfile.NamedTemporaryFile()
69 fout_t = tempfile.NamedTemporaryFile()
70 fout_g = tempfile.NamedTemporaryFile()
71 fout_c = tempfile.NamedTemporaryFile()
72 fout_ref = tempfile.NamedTemporaryFile()
73
74 fout_a.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
75 % ( "Track A", sdescription, '255,0,0', svisibility ))
76 fout_t.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
77 % ( "Track T", sdescription, '0,255,0', svisibility ))
78 fout_g.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
79 % ( "Track G", sdescription, '0,0,255', svisibility ))
80 fout_c.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
81 % ( "Track C", sdescription, '255,0,255', svisibility ))
82
83
84 sorted_infile.seek(0)
85 for line in file( sorted_infile.name ):
86 line = line.strip()
87 if not(line):
88 continue
89 try:
90 fields = line.split('\t')
91 chr = fields[chr_col]
92 start = int(fields[coord_col])
93 assert start > 0
94 except:
95 continue
96 try:
97 ind = chr_vals.index(chr) #encountered chr for the 1st time
98 del chr_vals[ind]
99 prev_start = ''
100 header = "variableStep chrom=%s\n" %(chr)
101 if track_type == 'coverage' or track_type == 'both':
102 coverage = int(fields[coverage_col])
103 line1 = "%s\t%s\n" %(start,coverage)
104 fout.write("%s%s" %(header,line1))
105 if track_type == 'snp' or track_type == 'both':
106 a = t = g = c = 0
107 fout_a.write("%s" %(header))
108 fout_t.write("%s" %(header))
109 fout_g.write("%s" %(header))
110 fout_c.write("%s" %(header))
111 try:
112 #ref_nt = fields[ref_col].capitalize()
113 read_nt = fields[read_col].capitalize()
114 try:
115 nt_ind = ['A','T','G','C'].index(read_nt)
116 if nt_ind == 0:
117 a+=1
118 elif nt_ind == 1:
119 t+=1
120 elif nt_ind == 2:
121 g+=1
122 else:
123 c+=1
124 except ValueError:
125 pass
126 except:
127 pass
128 prev_start = start
129 except ValueError:
130 if start != prev_start:
131 if track_type == 'coverage' or track_type == 'both':
132 coverage = int(fields[coverage_col])
133 fout.write("%s\t%s\n" %(start,coverage))
134 if track_type == 'snp' or track_type == 'both':
135 if a:
136 fout_a.write("%s\t%s\n" %(prev_start,a))
137 if t:
138 fout_t.write("%s\t%s\n" %(prev_start,t))
139 if g:
140 fout_g.write("%s\t%s\n" %(prev_start,g))
141 if c:
142 fout_c.write("%s\t%s\n" %(prev_start,c))
143 a = t = g = c = 0
144 try:
145 #ref_nt = fields[ref_col].capitalize()
146 read_nt = fields[read_col].capitalize()
147 try:
148 nt_ind = ['A','T','G','C'].index(read_nt)
149 if nt_ind == 0:
150 a+=1
151 elif nt_ind == 1:
152 t+=1
153 elif nt_ind == 2:
154 g+=1
155 else:
156 c+=1
157 except ValueError:
158 pass
159 except:
160 pass
161 prev_start = start
162 else:
163 if track_type == 'snp' or track_type == 'both':
164 try:
165 #ref_nt = fields[ref_col].capitalize()
166 read_nt = fields[read_col].capitalize()
167 try:
168 nt_ind = ['A','T','G','C'].index(read_nt)
169 if nt_ind == 0:
170 a+=1
171 elif nt_ind == 1:
172 t+=1
173 elif nt_ind == 2:
174 g+=1
175 else:
176 c+=1
177 except ValueError:
178 pass
179 except:
180 pass
181
182 if track_type == 'snp' or track_type == 'both':
183 if a:
184 fout_a.write("%s\t%s\n" %(prev_start,a))
185 if t:
186 fout_t.write("%s\t%s\n" %(prev_start,t))
187 if g:
188 fout_g.write("%s\t%s\n" %(prev_start,g))
189 if c:
190 fout_c.write("%s\t%s\n" %(prev_start,c))
191
192 fout_a.seek(0)
193 fout_g.seek(0)
194 fout_t.seek(0)
195 fout_c.seek(0)
196
197 if track_type == 'snp':
198 os.system("cat %s %s %s %s >> %s" %(fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname))
199 elif track_type == 'both':
200 fout.seek(0)
201 os.system("cat %s %s %s %s %s | cat > %s" %(fout.name,fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname))
202 if __name__ == "__main__":
203 main()