Mercurial > repos > yating-l > rename_scaffolds

comparison rename.py @ 1:0d13e4410c3d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 68b7e251486853b77396932b588c20f389c366d2
author yating-l
date Mon, 18 Jun 2018 18:36:00 -0400
parents 65c9ce351343
children 8fdd3e06e1ec
comparison
equal deleted inserted replaced
0:65c9ce351343 1:0d13e4410c3d
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 from collections import OrderedDict 6 from collections import OrderedDict
6 7
7 def rename(inputfile, outputfile, indexfile): 8 def rename(inputfile, outputfile, writer):
8 namemap = OrderedDict() 9 namemap = OrderedDict()
9 with open(outputfile, 'w') as out: 10 with open(outputfile, 'w') as out:
10 with open(inputfile, 'r') as rf: 11 with open(inputfile, 'r') as rf:
11 lines = rf.readlines() 12 lines = rf.readlines()
12 i = 1 13 i = 1
14 if ">" in line: 15 if ">" in line:
15 oldname = line[1:].rstrip() 16 oldname = line[1:].rstrip()
16 newname = "scaffold_" + str(i) 17 newname = "scaffold_" + str(i)
17 line = ">" + newname 18 line = ">" + newname
18 i = i+1 19 i = i+1
19 namemap[oldname] = newname 20 writer.writerow([oldname, newname])
20 #TODO: Add line breaks to chromosome sequences that are in a single line 21 #TODO: Add line breaks to chromosome sequences that are in a single line
21 #else:
22 #if (len(line) > 50):
23 #for
24 out.write(line.rstrip() + "\n") 22 out.write(line.rstrip() + "\n")
25 with open(indexfile, 'w') as index:
26 for k in namemap:
27 index.write(k + "\t" + namemap[k] + "\n")
28 23
29 def main(): 24 def main():
30 inputfile = str(sys.argv[1]) 25 inputfile = str(sys.argv[1])
31 outputfile = str(sys.argv[2]) 26 outputfile = str(sys.argv[2])
32 indexfile = str(sys.argv[3]) 27 indexfile = str(sys.argv[3])
33 rename(inputfile, outputfile, indexfile) 28 csvfile = open(indexfile, 'w')
29 fieldnames = ['Original sequence name', 'Renamed sequence name']
30 writer = csv.writer(csvfile)
31 writer.writerow(fieldnames)
32 rename(inputfile, outputfile, writer)
34 33
35 if __name__ == "__main__": 34 if __name__ == "__main__":
36 main() 35 main()
37 36
38 37