54 lines
1.2 KiB
Python
54 lines
1.2 KiB
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 re
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from time import sleep
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import requests
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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.split("_")[0] + ".fasta"
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response = requests.get(url)
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if response.status_code != 200:
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print(f"uniprot request failed for {i}")
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print(f"detail: {response.text}")
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fasta = response.text.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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sleep(1)
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# close output file
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f1.close()
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