Mercurial > repos > rreumerman > snptools

comparison tablemerger.py @ 4:bd5692103d5b draft

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author rreumerman
date Fri, 05 Apr 2013 05:00:40 -0400
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children 8de0ffc2166f
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3:a808647d7312 4:bd5692103d5b
1 '''Takes tab-delimited SNP tables from user input and merges them into one.'''
2
3 import sys
4 files = []
5 filenames = []
6
7 try:
8 output = open(sys.argv[1], "w")
9 output.write('Position\tReference')
10 except:
11 exit("No output file given or unable to open output file.")
12 for name in sys.argv[2:]:
13 try:
14 files.append(open(name, "rU"))
15 except:
16 continue
17
18 # Fetch headers and print them to output file;
19 headers = [header.readline()[:-1].split('\t')[2:] for header in files]
20 columns = [len(strains) for strains in headers]
21 for strain in [a for b in headers for a in b]:
22 output.write('\t'+strain)
23 output.flush()
24
25 file_active = [True]*len(files)
26 snps = [row.readline()[:-1].split('\t') for row in files]
27
28 while True in file_active:
29 for h in range(0,len(snps)):
30 if file_active[h]:
31 cur_pos = [h]
32 lowest = int(snps[h][0])
33 break
34 i = 1
35
36 # Determine lowest position
37 while i < len(snps):
38 if int(snps[i][0]) < lowest and file_active[i]:
39 lowest = int(snps[i][0])
40 cur_pos = [i]
41 elif int(snps[i][0]) == lowest:
42 cur_pos.append(i)
43 i+=1
44
45 # Check if all SNPs sharing a position have the same reference base, exit with message otherwise;
46 if len(cur_pos) > 1:
47 ref_base = snps[cur_pos[0]][1].lower()
48 for j in cur_pos[1:]:
49 if snps[j][1].lower() != ref_base:
50 error = '\nError: Reference bases not the same for position %s, present in following files:' % lowest
51 for k in cur_pos:
52 error += ' '+filenames[k]
53 exit(error+'.')
54
55 # Write line to output file containing position, ref base and snps/empty cells;
56 output.write('\n'+snps[cur_pos[0]][0]+'\t'+snps[cur_pos[0]][1].lower())
57 for l,row in enumerate(snps):
58 if l in cur_pos:
59 for snp in row[2:]:
60 output.write('\t'+snp)
61 else:
62 output.write('\t'*columns[l])
63
64 # Read new line in files that had snp at current position;
65 for m in cur_pos:
66 line = files[m].readline()
67 if line == '': file_active[m] = False
68 else:
69 snps[m] = line.split('\t')
70 snps[m][-1] = snps[m][-1].rstrip()# Remove newline character at end of line;
71
72 for it in files: it.close()
73 output.close()