Mercurial > repos > yating-l > rename_scaffolds
comparison rename.py @ 2:8fdd3e06e1ec draft
planemo upload commit eb7c6866b218a41d9b22255ee6afb83551a5ff40
author | yating-l |
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date | Mon, 25 Jun 2018 15:29:18 -0400 |
parents | 0d13e4410c3d |
children | 9529a207d704 |
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1:0d13e4410c3d | 2:8fdd3e06e1ec |
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1 """ | 1 """ |
2 Call rename to rename scaffolds in reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and provide a name mapping file | 2 Call rename to rename scaffolds in reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and provide a name mapping file |
3 """ | 3 """ |
4 import sys | 4 import sys |
5 import csv | 5 import csv |
6 from collections import OrderedDict | |
7 | 6 |
8 def rename(inputfile, outputfile, writer): | 7 def rename(inputfile, outputfile, writer): |
9 namemap = OrderedDict() | |
10 with open(outputfile, 'w') as out: | 8 with open(outputfile, 'w') as out: |
11 with open(inputfile, 'r') as rf: | 9 with open(inputfile, 'r') as rf: |
12 lines = rf.readlines() | 10 lines = rf.readlines() |
13 i = 1 | 11 i = 1 |
14 for line in lines: | 12 for line in lines: |
15 if ">" in line: | 13 if ">" in line: |
16 oldname = line[1:].rstrip() | 14 oldname = line[1:].rstrip() |
17 newname = "scaffold_" + str(i) | 15 newname = "scaffold_" + str(i) |
18 line = ">" + newname | 16 line = ">" + newname + "\n" |
19 i = i+1 | 17 i = i+1 |
20 writer.writerow([oldname, newname]) | 18 writer.writerow([oldname, newname]) |
21 #TODO: Add line breaks to chromosome sequences that are in a single line | 19 out.write(line) |
22 out.write(line.rstrip() + "\n") | |
23 | 20 |
24 def main(): | 21 def main(): |
25 inputfile = str(sys.argv[1]) | 22 inputfile = str(sys.argv[1]) |
26 outputfile = str(sys.argv[2]) | 23 outputfile = str(sys.argv[2]) |
27 indexfile = str(sys.argv[3]) | 24 indexfile = str(sys.argv[3]) |
28 csvfile = open(indexfile, 'w') | 25 csvfile = open(indexfile, 'w') |
29 fieldnames = ['Original sequence name', 'Renamed sequence name'] | |
30 writer = csv.writer(csvfile) | 26 writer = csv.writer(csvfile) |
31 writer.writerow(fieldnames) | |
32 rename(inputfile, outputfile, writer) | 27 rename(inputfile, outputfile, writer) |
33 | 28 |
34 if __name__ == "__main__": | 29 if __name__ == "__main__": |
35 main() | 30 main() |
36 | 31 |