from optparse import OptionParser
#
# Parse the options
#
option_parser = OptionParser()
option_parser.add_option(
"-n",
"--num-seqs",
dest="num_seqs",
default=10,
type='int',
help="Number of sequences to output."
)
options, args = option_parser.parse_args()
#
# Check args
#
if 1 != len(args):
print >> sys.stderr, 'USAGE: %s <fasta file>' % __file__
sys.exit(-1)
fasta = args[0]
if '-' == fasta:
input = sys.stdin
else:
input = open(fasta, 'r')
for i, seq in zip(xrange(options.num_seqs), F.iterseq(input, corebio.seq.dna_alphabet)):
F.writeseq(sys.stdout, seq)
"""
Code that reads in 2 sets of sequences and outputs those in the first that are not in the second.
"""
import sys, corebio.seq_io.fasta_io as F, corebio.seq
from optparse import OptionParser
#
# Parse the options
#
option_parser = OptionParser()
options, args = option_parser.parse_args()
#
# Check args
#
if 2 != len(args):
print >> sys.stderr, 'USAGE: %s <fasta file> <fasta file>' % __file__
sys.exit(-1)
fasta1, fasta2 = args
# read in second fasta
to_subtract = set(
seq.description.strip().lower()
for seq in F.iterseq(open(fasta2, 'r'), corebio.seq.dna_alphabet))
# read in first fasta
for seq in F.iterseq(open(fasta1, 'r'), corebio.seq.dna_alphabet):
if seq.description.strip().lower() not in to_subtract:
F.writeseq(sys.stdout, seq)
option_parser.add_option('-m',
'--max-sequences',
dest='max_seqs',
type='int',
default=-1,
help="Set a limit on the number of sequences output.")
options, args = option_parser.parse_args()
#
# Check args
#
if 2 != len(args):
print >> sys.stderr, 'USAGE: %s <fasta file> <max sequence length>' % __file__
sys.exit(-1)
fasta = args[0]
length = int(args[1])
if '-' == fasta:
input = sys.stdin
else:
input = open(fasta, 'r')
#
# Read the sequences
#
alphabet = corebio.seq.reduced_nucleic_alphabet
for i, seq in enumerate(F.iterseq(input, alphabet)):
if options.max_seqs == i:
break
F.writeseq(sys.stdout, shorten(seq))
'--max-sequences',
dest='max_seqs',
type='int',
default=-1,
help="Set a limit on the number of sequences output."
)
options, args = option_parser.parse_args()
#
# Check args
#
if 2 != len(args):
print >> sys.stderr, 'USAGE: %s <fasta file> <max sequence length>' % __file__
sys.exit(-1)
fasta = args[0]
length = int(args[1])
if '-' == fasta:
input = sys.stdin
else:
input = open(fasta, 'r')
#
# Read the sequences
#
alphabet = corebio.seq.reduced_nucleic_alphabet
for i, seq in enumerate(F.iterseq(input, alphabet)):
if options.max_seqs == i:
break
F.writeseq(sys.stdout, shorten(seq))
shuffled.name = '%s (shuffled)' % seq.name,
shuffled.description = '%s (shuffled)' % seq.description,
shuffled.alphabet = seq.alphabet
return shuffled
#
# Parse the options
#
option_parser = OptionParser()
options, args = option_parser.parse_args()
#
# Check args
#
if 1 != len(args):
print >> sys.stderr, 'USAGE: %s <fasta file>' % __file__
sys.exit(-1)
fasta = args[0]
#
# Shuffle the sequences
#
for seq in F.iterseq(
open(fasta, 'r'),
corebio.seq.dna_alphabet
):
F.writeseq(sys.stdout, shuffle(seq))