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 render(args, outfile):
def parse_key(l):
regex = re.compile(r'[^>\s\n]+')
mat = regex.search(l)
return mat and mat.group() or None
recgens = [fasta.read(fn, False) for fn in args.filenames]
records = itertools.chain(*recgens)
if not args.order:
keys = {parse_key(l) for l in open(args.listfile)}
for rec in records:
cmt = rec.cmt.split()[0]
if cmt in keys:
outrec = dict(cmt=cmt, seq=rec.seq) if args.concise else rec
fasta.write(outfile, outrec)
return # simple and fast
if args.order: # ^ in case of accidental deletion of that return
# preserve order of keys in list file
keys = (parse_key(l) for l in open(args.listfile))
selection = collections.OrderedDict((k, None) for k in keys if k)
for rec in records:
# use title.split()[0] to be tolerent to titles with description
cmt = rec.cmt.split()[0]
# this consumes a lot of memory
if cmt in selection:
selection[cmt] = rec
for cmt in selection:
rec = selection[cmt]
outrec = dict(cmt=cmt, seq=rec.seq) if args.concise else rec
fasta.write(outfile, outrec)
def render(cls, args, outfile):
compl = CharsMapper.create_mapper_compl_dna()
for fn in args.filenames:
for rec in fasta.read(fn):
rec.cmt += ".RC"
rec.seq = compl.transcode(rec.seq)[::-1]
fasta.write(outfile, rec)
def render(cls, args, outfile):
recgens = [fasta.read(fn) for fn in args.filenames]
records = itertools.chain(*recgens)
for r in records:
text = primer.render_primer3_input(rec=r)
if not text.endswith('\n'):
text += '\n'
outfile.write(text)
def process(cls, args, outfile, filename):
seqrecords = fasta.read(filename)
for rec in seqrecords:
gc = statis.calc_gc_content(rec['seq'])
if args.percent:
gc *= 100
line = '{0:.{1}f}\t{2}\n'.format(gc, args.precision, rec['cmt'])
outfile.write(line)
def render(cls, args, outfile):
dic = translate.get_transl_table(args.table)
tab = CodonTable(dic)
for fn in args.filenames:
for rec in fasta.read(fn, args.concise):
if len(rec.seq) % 3:
if not args.quiet:
msg = 'warning: lenth of seq not a multiple of 3\n'
msg += '^debug:\t{}\t{}\t{}'.format(len(rec.seq), fn, rec.cmt)
print(msg, file=sys.stderr)
if args.skip:
continue
l = len(rec.seq)
rec.seq = rec.seq[:int(l - l % 3)]
rec.seq = tab.translate(rec.seq)
fasta.write(outfile, rec)
def test_align():
istring, jstring, submatr = submat.read('pam200')
ali = aligner.Aligner.from_submatr(istring, jstring, submatr)
path = locate_tests('data/rmlA.2x.fa')
iseq, jseq = fasta.read(path, castfunc=lambda x: [s.seq for s in x])
with Timer('align'):
for i in range(repeat):
matrx, istring, jstring = ali.align(iseq, jseq, backtrack=True)
mstring = aligner.gen_match_string(istring, jstring)
for items in molbiox.frame.streaming.chunkwise(60, istring, mstring, jstring):
bunch = six.b('\n').join(items).decode('ascii')
print(bunch, end='\n\n', file=sys.stderr)
def process(cls, args, outfile, filename):
seqrecords = fasta.read(filename)
for rec in seqrecords:
line = '{}\t{}\n'.format(len(rec.seq), rec.cmt)
outfile.write(line)