Mercurial > repos > rdvelazquez > rdv_fasta_tools

comparison filterFasta @ 0:146ffed44f3f draft default tip

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planemo upload
author rdvelazquez
date Wed, 20 Mar 2019 22:17:40 -0400
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-1:000000000000 0:146ffed44f3f
1 #!/usr/bin/env python3
2
3 import sys
4
5 # first argument is script name
6 # second should be fasta path
7 # third should be minimum number of non-gap characters required to be in seq
8 # fourth argument should be the path to save the fasta at
9 originalFastaPath = sys.argv[1]
10 minNumNonGapChars = int(sys.argv[2])
11 newFastaPath = sys.argv[3]
12
13 filteredFastaString = ""
14
15 with open(originalFastaPath) as fp:
16 line = fp.readline()
17 cnt = 1
18 while line:
19 if line.startswith(">"):
20 id = line
21 else:
22 sequence = line
23 numNonGapChars = len( line.replace("-","") )
24 if numNonGapChars >= minNumNonGapChars:
25 filteredFastaString += id + sequence
26 line = fp.readline()
27 cnt += 1
28
29 f = open(newFastaPath, "w")
30 f.write(filteredFastaString)