45 lines
929 B
Python
45 lines
929 B
Python
#!/usr/bin/python
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#MPRT - Finding a Protein Motif Solution
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#Problem can be found at http://rosalind.info/problems/mprt/
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#Author: Peter Vlasveld
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import urllib2
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import re
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#declare motif
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motif = "N[^P][ST][^P]"
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#read in file
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f0 = open("rosalind_mprt.txt", "r")
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content = f0.read().splitlines()
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f0.close()
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#open output file
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f1 = open("output.txt", "w+")
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#loop through each accession ID
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for i in content:
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#get fasta from url
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url = "http://www.uniprot.org/uniprot/" + i + ".fasta"
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response = urllib2.urlopen(url)
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fasta = response.read().splitlines()
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#format protein string
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protStr = ""
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for j in fasta:
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if not j.startswith('>'):
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protStr += j
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#construct output strings
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outStr = ""
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for j in range(0, len(protStr)-4):
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if re.match(motif,protStr[j:j+4]):
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outStr += str(j+1) + " "
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#output
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if not outStr == "":
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print i
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f1.write(i + "\n")
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print outStr
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f1.write(outStr + "\n")
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#close output file
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f1.close()
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