def main():
try:
input_file = sys.argv[1]
fasta_file = sys.argv[2]
except IndexError:
print >> sys.stderr, \
'unmapped_seq2.py <text file> <fasta file> [min length=50]'
try:
min_length = int(sys.argv[3])
except IndexError:
min_length = 50
db = seqdb.SequenceFileDB(fasta_file)
input_sequences = set()
print >> sys.stderr, 'Reading sequences...',
for line in open(input_file):
input_sequences.add(line.strip())
print >> sys.stderr, 'total %d' % len(input_sequences)
print >> sys.stderr, 'Writing unmapped sequences...'
for seq in db:
sequence = db[seq]
if (seq not in input_sequences and len(sequence) >= min_length):
print >> sys.stderr, 'Writing %s, %d bp' % (seq, len(sequence))
sequtil.write_fasta(sys.stdout, str(sequence), id=seq)
def write_seq(filename, genome, output, strand):
reader = csv.reader(open(filename), dialect='excel-tab')
for n, line in enumerate(reader, start=1):
chrom = line[0]
chrom_start = int(line[1])
gene_id = line[3]
exon_starts = [int(start) + \
chrom_start for start in line[-1].split(',')]
exon_sizes = [int(size) for size in line[-2].split(',')]
exon_ends = [exon_starts[i] + \
exon_sizes[i] for i in range(len(exon_starts))]
exons = [Exon(chrom, exon_starts[i], exon_ends[i]) for i in \
range(len(exon_starts))]
strand = 'negative' if line[5] == '-' else 'positive'
if output == 'transcript':
seq = get_sequence_transcript(genome, exons, strand)
sequtil.write_fasta(sys.stdout, seq, id=gene_id)
elif output == 'exon':
seqs = get_sequence_exon(genome, exons, strand)
for n, seq in enumerate(seqs, start=1):
seq_id = gene_id + '_' + str(n)
sequtil.write_fasta(sys.stdout, seq, id=seq_id)
else:
print >> sys.stderr, 'Unsupported output format.'
raise SystemExit
if n % 1000 == 0:
print >> sys.stderr, '...', n
def main():
try:
input_file = sys.argv[1]
fasta_file = sys.argv[2]
except IndexError:
print >> sys.stderr, \
'unmapped_seq2.py <text file> <fasta file> [min length=50]'
try:
min_length = int(sys.argv[3])
except IndexError:
min_length = 50
db = seqdb.SequenceFileDB(fasta_file)
input_sequences = set()
print >> sys.stderr, 'Reading sequences...',
for line in open(input_file):
input_sequences.add(line.strip())
print >> sys.stderr, 'total %d' % len(input_sequences)
print >> sys.stderr, 'Writing unmapped sequences...'
for seq in db:
sequence = db[seq]
if (seq not in input_sequences and len(sequence) >= min_length):
print >> sys.stderr, 'Writing %s, %d bp' % (seq, len(sequence))
sequtil.write_fasta(sys.stdout, str(sequence), id=seq)
def main():
filename = sys.argv[1]
genome = seqdb.SequenceFileDB(sys.argv[2], verbose=False)
for n, (exons, gene_id) in enumerate(
parse_seq(filename, genome), start=1):
seq = get_sequence(genome, exons)
sequtil.write_fasta(sys.stdout, seq, id=gene_id)
if n % 1000 == 0:
print >> sys.stderr, '...', n
def write_sequence(source, graph, targets, queries, ofile1, ofile2):
visited_nodes = set()
max_length = 0
for node in nx.algorithms.dfs_preorder_nodes(graph, source):
seq = targets[node] if node in targets else queries[node]
if len(seq) > max_length: max_length = len(seq)
if node in targets:
sequtil.write_fasta(ofile1, str(seq), 60, node)
else:
sequtil.write_fasta(ofile2, str(seq), 60, node)
visited_nodes.add(node)
return visited_nodes, max_length
def write_sequence(source, graph, targets, queries, ofile1, ofile2):
visited_nodes = set()
max_length = 0
for node in nx.algorithms.dfs_preorder_nodes(graph, source):
seq = targets[node] if node in targets else queries[node]
if len(seq) > max_length: max_length = len(seq)
if node in targets:
sequtil.write_fasta(ofile1, str(seq), 60, node)
else:
sequtil.write_fasta(ofile2, str(seq), 60, node)
visited_nodes.add(node)
return visited_nodes, max_length
def get_sequence(infile, genome):
reader = csv.reader(open(infile), dialect='excel-tab')
for rec in reader:
attrs = dict([
(key, value)
for key, value in [item.split('=') for item in rec[-1].split(';')]
])
exon_start = int(attrs["exonStart"]) - 1
exon_end = int(attrs["exonEnd"])
chrom = rec[0]
strand = attrs["strand"]
id = attrs["ID"]
exon_seq = genome[chrom][exon_start:exon_end]
if strand == '-':
exon_seq = str(-exon_seq)
else:
exon_seq = str(exon_seq)
sequtil.write_fasta(sys.stdout, exon_seq, id=id)
def get_sequence(cluster_trees, fasta_file, trans_db):
print >> sys.stderr, 'reading %s' % fasta_file
sequences = seqdb.SequenceFileDB(fasta_file, verbose=False)
cluster_no = 0
for chrom, cluster_tree in cluster_trees.items():
for start, end, trans_nos in cluster_tree.getregions():
print >> sys.stderr, '%d\t%s:%d-%d\t%d' \
% (cluster_no, chrom, start, end, len(trans_nos))
with open('locus_%d.fa' % (cluster_no), 'w') as op:
for no in trans_nos:
seqid = trans_db[no].trans_id
try:
sequence = sequences[seqid].seq
except KeyError:
pass
else:
sequtil.write_fasta(
op,
sequence,
id=seqid,
)
cluster_no += 1
import sys
from pygr import seqdb, sequtil
inputFile = sys.argv[1]
genome = seqdb.SequenceFileDB(sys.argv[2])
for n, line in enumerate(open(inputFile), start=1):
features = line.split()
chrom = features[0]
start = int(features[3]) - 1
end = start + 150
snpid = "%s:%d" % (chrom, start)
seq = genome[chrom][start:end]
sequtil.write_fasta(sys.stdout, seq, id=snpid)
if (n % 1000) == 0:
print >> sys.stderr, '...', n
'''
import sys
from pygr import seqdb, sequtil
if len(sys.argv) < 4:
print >> sys.stderr, \
'Usage: split_sequence.py fasta_file chunk_size overlap_size'
raise SystemExit
input_file = sys.argv[1]
chunk_size = int(sys.argv[2])
overlap_size = int(sys.argv[3])
db = seqdb.SequenceFileDB(input_file)
for seq in db:
window = 0
print >> sys.stderr, 'Splitting %s...' % (seq)
if len(db[seq]) <= chunk_size:
sequtil.write_fasta(sys.stdout, str(db[seq]), id=seq)
else:
seq = db[seq]
_id = 1
chunk_id = "%s_%d" % (seq.id, _id)
while window < len(seq):
chunk = seq[window:window + chunk_size]
sequtil.write_fasta(sys.stdout, str(chunk), id=chunk_id)
_id += 1
window += (chunk_size - overlap_size)
'''Get a part of a target sequence that aligned to a given query sequence.'''
import sys
import csv
from pygr import seqdb, sequtil
psl_file = sys.argv[1]
genome_file = sys.argv[2]
genome = seqdb.SequenceFileDB(genome_file)
reader = csv.reader(open(psl_file), dialect='excel-tab')
for cols in reader:
target = cols[13]
start = int(cols[15])
end = int(cols[16])
seq = genome[target][start:end]
seqid = target + '_' + cols[9]
sequtil.write_fasta(sys.stdout, str(seq), id=seqid)
