Mercurial > repos > rnateam > rnacommender

comparison rbpfeatures.py @ 4:a609d6dc8047 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
author rnateam
date Thu, 28 Jul 2016 05:55:25 -0400
parents 8918de535391
children
comparison
equal deleted inserted replaced
3:ecf125a1ad73 4:a609d6dc8047
1 """Compute the RBP features.""" 1 """Compute the RBP features."""
2 2
3 import re 3 import re
4 import sys
4 import subprocess as sp 5 import subprocess as sp
5 import uuid 6 import uuid
6 from os import mkdir 7 from os import mkdir
7 from os import listdir 8 from os import listdir
8 from os.path import isfile, join 9 from os.path import isfile, join
54 """Scan the sequences against the Pfam database.""" 55 """Scan the sequences against the Pfam database."""
55 nf = open(self.pfam_scan, "w") 56 nf = open(self.pfam_scan, "w")
56 nf.write(pfam_utils.search_header()) 57 nf.write(pfam_utils.search_header())
57 58
58 fasta = fasta_utils.import_fasta(self.fasta) 59 fasta = fasta_utils.import_fasta(self.fasta)
60
61 if len(fasta) != 1:
62 sys.exit("""Fasta file must contain exactly one sequence.""")
59 63
60 for rbp in sorted(fasta.keys()): 64 for rbp in sorted(fasta.keys()):
61 seq = fasta[rbp] 65 seq = fasta[rbp]
62 text = pfam_utils.sequence_search(rbp, seq) 66 text = pfam_utils.sequence_search(rbp, seq)
63 nf.write(text) 67 nf.write(text)