def read_blast(blast_file, qorder, sorder, is_self=False):
"""
read the blast and convert name into coordinates
"""
fp = open(blast_file)
filtered_blast = []
seen = set()
for row in fp:
b = BlastLine(row)
query, subject = b.query, b.subject
if query not in qorder or subject not in sorder:
continue
key = query, subject
if key in seen:
continue
seen.add(key)
qi, q = qorder[query]
si, s = sorder[subject]
if is_self and qi > si:
# remove redundant a<->b to one side when doing self-self BLAST
query, subject = subject, query
qi, si = si, qi
q, s = s, q
b.qseqid, b.sseqid = q.seqid, s.seqid
b.qi, b.si = qi, si
filtered_blast.append(b)
return filtered_blast
def read_blast(blast_file, qorder, sorder, is_self=False):
"""
read the blast and convert name into coordinates
"""
fp = open(blast_file)
filtered_blast = []
seen = set()
for row in fp:
b = BlastLine(row)
query, subject = b.query, b.subject
if query not in qorder or subject not in sorder:
continue
key = query, subject
if key in seen:
continue
seen.add(key)
qi, q = qorder[query]
si, s = sorder[subject]
if is_self and qi > si:
# remove redundant a<->b to one side when doing self-self BLAST
query, subject = subject, query
qi, si = si, qi
q, s = s, q
b.qseqid, b.sseqid = q.seqid, s.seqid
b.qi, b.si = qi, si
filtered_blast.append(b)
return filtered_blast
def read_blast(blast_file, qorder, sorder, is_self=False, ostrip=True):
"""
read the blast and convert name into coordinates
"""
fp = open(blast_file)
filtered_blast = []
seen = set()
for row in fp:
b = BlastLine(row)
query, subject = b.query, b.subject
if query == subject:
continue
if ostrip:
query, subject = gene_name(query), gene_name(subject)
if query not in qorder or subject not in sorder:
continue
qi, q = qorder[query]
si, s = sorder[subject]
if is_self and qi > si:
# remove redundant a<->b to one side when doing self-self BLAST
query, subject = subject, query
qi, si = si, qi
q, s = s, q
key = query, subject
if key in seen:
continue
seen.add(key)
b.qseqid, b.sseqid = q.seqid, s.seqid
b.qi, b.si = qi, si
b.query, b.subject = query, subject
filtered_blast.append(b)
logging.debug("A total of {0} BLAST imported from `{1}`.".\
format(len(filtered_blast), blast_file))
return filtered_blast
def read_blast(blast_file, qorder, sorder, is_self=False, ostrip=True):
"""
read the blast and convert name into coordinates
"""
fp = open(blast_file)
filtered_blast = []
seen = set()
for row in fp:
b = BlastLine(row)
query, subject = b.query, b.subject
if query == subject:
continue
if ostrip:
query, subject = gene_name(query), gene_name(subject)
if query not in qorder or subject not in sorder:
continue
qi, q = qorder[query]
si, s = sorder[subject]
if is_self and qi > si:
# remove redundant a<->b to one side when doing self-self BLAST
query, subject = subject, query
qi, si = si, qi
q, s = s, q
key = query, subject
if key in seen:
continue
seen.add(key)
b.qseqid, b.sseqid = q.seqid, s.seqid
b.qi, b.si = qi, si
b.query, b.subject = query, subject
filtered_blast.append(b)
logging.debug("A total of {0} BLAST imported from `{1}`.".\
format(len(filtered_blast), blast_file))
return filtered_blast