def render(cls, args, outfile):
if args.regex and args.regex[0] not in 'exs':
msg = """
possible regex forms:
1. 'm/pattern/modifiers' - select matching ones
2. 'x/pattern/modifiers' - select non-matching ones
3. 's/pattern/repl/modifiers' - apply replacement on cmt
"""
print(msg, file=sys.stderr)
sys.exit('error: invalid regex')
for fn in args.filenames:
recs = fasta.read(fn, args.concise)
if args.velvet:
recs = cls.filter_velvet_concise(recs)
if args.insert_filename:
ifn = args.insert_filename
recs = cls.filter_insert_filename(recs, fn, ifn)
if args.regex:
try:
regexon = Regexon.perl(args.regex)
except ValueError as e:
sys.exit(e)
recs = cls.filter_regex(recs, regexon)
fasta.write(outfile, recs, linewidth=args.width)
def filter_insert_filename(cls, recs, filename, position):
name = filename.split('.')[0]
regs = {
'head': r's/^([^\s]+)/{}.\1/'.format(name),
'tail': r's/^([^\s]+)/\1.{}/'.format(name),
}
regexon = Regexon.perl(regs[position])
return cls.filter_regex(recs, regexon)
from __future__ import print_function
import os
import unittest
from molbiox.algor.translate import CodonTable
from molbiox.frame.signature import Sig
from molbiox.frame.regexon import Regexon
from molbiox.kb.translate import get_transl_table
sub = Regexon.new(r'[^a-zA-Z]', '')
test_data = {
'dna': """
TTGATGGCTAAGAGTAAAATCTTAAAAAACACACTGGTTCTATATTTTCGTCAAGTTTTG
ATTGTATTAATTACTCTCTATTCAATGAGAGTTGTATTAAATGAATTAGGTGTGGATGAT
TTTGGTATTTATAGCGTTGTGGCTGGTTTTGTAACTTTACTTGCATTTTTACCCGGAAGC
ATGGCGAGTGCAACGCAGCGGTTTTTCTCTTTTGCGATGGGGAAATCGGATATAGTAAAA
TTAAAGCAAACCTTCAGTGTTAATTTAGTTATGTATACTGGCATAGCCTTGTTAGCATAT
ATAACATTTCAAACTATCGGATTTTGGTATGTTGATGAATATCTAAAAATACCTCATAAC
CGCTTTCATGCAGCCTTGGAATTATATCACTATGTGTCTTTATCATTTATTTTTTCAATT
TTTTCTGCGCCTTTTATCGCGATTTTAATTGCGCACGAAGATATGCACATTTATGCGATC
TTCTCGGTTTTTGATGCATTTTTAAAACTAGTAGCCGCAATTTCTTTAGACTATGTGAAC
TATGATTTGTTAGCTTATTATGGAGTGGCTCTTTTGATTGTATCTGGATTGCTTGCTTTC
GCGTATATTTTTATATGTATAAAGAAATATCCAGAGTGTCAAATGAAAAAGCTTTATTGG
AGTTCGAGTATACTGAAAGAAATTATTGGTTTCACGATATGGACTTTGCTAGGTCAATTG
AGCACTGTTTTTAGAAATCAGGCAGTAACTGTTCTTGTAAACCAAATGTTTAATCCTTCA
ATTGTGGCAGCTCGTGCAATTGCCTTGAATGTGGCTAGTCAAGTTGGAATTTTTTCGAAT
AATTTAAATACAGGGTTATATCCACCAATTATAAAAGCTTACGCAGCAAATCAAAAAGAG
GAAATGCTGAGTTTAGTTTTTAATGGTTCTAAACTGACTTTCTTCTTGATGTGGGTATGT
GCATTACCCATGTTGCTTGAAATGGAAACGATATTAACACTTTGGCTAAAAACACCACCA
TCAGAAGCGATATTATTTACTCAGTTAGCGATTGTTGAATCCTTGATACTGGCTATAAGC