Mercurial > repos > bgruening > protein_properties
comparison protein_properties.py @ 0:cd211b8c2e51 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties commit 6767a5ffb02052c844e9d862c79912f998f39d8e
| author | bgruening |
|---|---|
| date | Mon, 20 Nov 2017 05:09:21 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:cd211b8c2e51 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 import sys | |
| 4 from Bio import SeqIO | |
| 5 from Bio.SeqUtils.ProtParam import ProteinAnalysis | |
| 6 | |
| 7 sys.stdout.write("ID\tMW\tIP\tgravy\tlength\tinstability\tmonoisotpoic\tSequence\n") | |
| 8 | |
| 9 for record in SeqIO.parse(sys.stdin, "fasta"): | |
| 10 a = ProteinAnalysis(str(record.seq)) | |
| 11 | |
| 12 properties = list() | |
| 13 properties.append(record.id) | |
| 14 properties.append(a.molecular_weight()) | |
| 15 properties.append(a.isoelectric_point()) | |
| 16 properties.append(a.gravy()) | |
| 17 properties.append(a.length) | |
| 18 properties.append(a.instability_index()) | |
| 19 properties.append(a.aromaticity()) | |
| 20 # always last column to make the output more readable | |
| 21 properties.append(a.sequence) | |
| 22 sys.stdout.write( '\t'.join(map(str, properties))+"\n" ) | |
| 23 |