Mercurial > repos > rdvelazquez > rdv_fasta_tools
diff addFileNameToFastaIDs @ 0:146ffed44f3f draft default tip
planemo upload
author | rdvelazquez |
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date | Wed, 20 Mar 2019 22:17:40 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/addFileNameToFastaIDs Wed Mar 20 22:17:40 2019 -0400 @@ -0,0 +1,28 @@ +#!/usr/bin/env python3 + +import sys + +# first argument is script name +# second should be fasta path +# third argument should be the text to prepend to the seq ids +# fourth argument should be the path to save the fasta at +originalFastaPath = sys.argv[1] +textToPrepend = sys.argv[2] +newFastaPath = sys.argv[3] + +newFastaString = "" + +with open(originalFastaPath) as fp: + line = fp.readline() + cnt = 1 + while line: + if line.startswith(">"): + id = ">" + textToPrepend + "_" + line[1:] + else: + sequence = line + newFastaString += id + sequence + line = fp.readline() + cnt += 1 + +f = open(newFastaPath, "w") +f.write(newFastaString)