def main(cnsfile, qfasta_file, sfasta_file, qorg, sorg, min_len):
"""empty docstring"""
lens = []
qfasta = Fasta(qfasta_file)
sfasta = Fasta(sfasta_file)
seen = {}
lens_append = lens.append
qseq, sseq = None, None
# so we only read a new fasta file as needed.
last_qchr, last_schr = None, None
seen = {}
for cns in CNS.parse_raw_line(cnsfile):
#if is_intron(cns,qbed): continue
qseq = qfasta[str(cns.qseqid)]
sseq = sfasta[str(cns.sseqid)]
sstart, send = sorted((cns.sstart, cns.sstop))
qkey = (cns.qseqid, cns.qstart, cns.qstop)
skey = (cns.sseqid, cns.sstart, cns.sstop)
assert sstart < send
if cns.qstop - cns.qstart < min_len: continue
if send - sstart < min_len: continue
if not (qkey in seen and skey in seen):
print ">q__" + cns.cns_id
seqstr = str(qseq[cns.qstart - 1:cns.qstop]).replace(
'R', 'N').replace('W', 'N').replace('M', 'N')
assert set(seqstr.lower()).issubset("actgnx"), ('q',
'q__' + cns.cns_id,
seqstr)
print seqstr.upper()
print ">s__" + cns.cns_id
seqstr = str(sseq[sstart - 1:send]).replace('R', 'N').replace(
'W', 'N').replace('M', 'N')
assert set(seqstr.lower()).issubset("actgnx"), ('s',
's__' + cns.cns_id,
seqstr)
print seqstr.upper()
seen[qkey] = 1
seen[skey] = 1
def main(blast_files, out_dir,raw_cns):
"""empty docstring"""
cns_by_id = {}
for cns in CNS.parse_raw_line(raw_cns):
cns_by_id[cns.cns_id] = cns
exons = collections.defaultdict(dict)
for blast_file in blast_files:
for line in open(blast_file):
b = BlastLine(line)
# chop the q__ and s__
key = b.query[3:]
#assert key == b.subject[3:], (key, b.subject[3:])
# convert piped rice names to short canonical names.
subject = b.subject.split("|")[0] if "|" in b.subject else b.subject
# chop At2g26540.1 to At2g26540
subject = subject[:-2] if subject[-2] == "." else subject
subject = subject.replace('LOC_', '')
if b.score > 50:
if not subject in exons[key]:
exons[key][subject] = [b.eval]
else:
exons[key][subject].append(b.eval)
continue
if b.score < 45: continue
cns = cns_by_id[key]
# qstart?
qlen = cns.qstop - cns.qstart
coverage = (b.hitlen * 3.) / qlen
#print >>sys.stderr, coverage
if coverage < 0.90: continue
if not subject in exons[key]:
exons[key][subject] = [b.eval]
else:
exons[key][subject].append(b.eval)
exons = dict(exons)
write_exons(exons, out_dir)
#for cns_hash, at_exons in exons.iteritems():
print >>sys.stderr, "%i total unique cnss are exons" % (len(exons), )
return exons
def main(cnsfile, qfasta_file, sfasta_file, qorg, sorg, min_len):
"""empty docstring"""
lens = []
qfasta = Fasta(qfasta_file)
sfasta = Fasta(sfasta_file)
seen = {}
lens_append = lens.append
qseq, sseq = None, None
# so we only read a new fasta file as needed.
last_qchr, last_schr = None, None
seen = {}
for cns in CNS.parse_raw_line(cnsfile):
#if is_intron(cns,qbed): continue
qseq = qfasta[str(cns.qseqid)]
sseq = sfasta[str(cns.sseqid)]
sstart, send = sorted((cns.sstart, cns.sstop))
qkey = (cns.qseqid, cns.qstart, cns.qstop)
skey = (cns.sseqid, cns.sstart, cns.sstop)
assert sstart < send
if cns.qstop - cns.qstart < min_len: continue
if send - sstart < min_len: continue
if not (qkey in seen and skey in seen):
print ">q__" + cns.cns_id
seqstr = str(qseq[cns.qstart - 1: cns.qstop]).replace('R', 'N').replace('W', 'N').replace('M', 'N')
assert set(seqstr.lower()).issubset("actgnx"), ('q', 'q__' + cns.cns_id, seqstr)
print seqstr.upper()
print ">s__" + cns.cns_id
seqstr = str(sseq[sstart - 1: send]).replace('R', 'N').replace('W', 'N').replace('M', 'N')
assert set(seqstr.lower()).issubset("actgnx"), ('s', 's__' + cns.cns_id, seqstr)
print seqstr.upper()
seen[qkey] = 1
seen[skey] = 1
def main(qbed_path, sbed_path, cnsfile, dist, orthology_path):
"""
here, we remove cnss that have been called proteins/rnas from
the cns list, and add them to the bed files.
AND have to do the preliminary assignment of cnss that remain to the new-genes
that _were_ cnss. the proper assignment is then handled in assign.py
"""
qcns_file = qbed_path.replace(".bed", "_cns.gff")
assert qcns_file != qbed_path
qcns_gff = open(qcns_file, 'w')
print >>qcns_gff, "##gff-version 3"
if sbed_path != qbed_path:
scns_file = sbed_path.replace(".bed", "_cns.gff")
assert scns_file != sbed_path
scns_gff = open(scns_file, 'w')
print >>scns_gff, "##gff-version 3"
else: scns_gff = qcns_gff
qrawbed = RawBed(qbed_path)
srawbed = RawBed(sbed_path)
ortho_trees = read_orthos_to_trees(orthology_path, qrawbed,srawbed)
qbed = Bed(qbed_path); qbed.fill_dict()
sbed = Bed(sbed_path); sbed.fill_dict()
name, ext = op.splitext(cnsfile)
real_cns_fh = open("%s.real%s" % (name, ext), "w")
print >>sys.stderr, "writing to:", real_cns_fh.name
outdir = op.dirname(cnsfile)
print >>real_cns_fh, "#qseqid,qaccn,sseqid,saccn,qstart,qend,sstart,send,eval"
crna = read_cns_to_rna(outdir)
cpro = read_cns_to_protein_exons(outdir)
#cns_items = list(parse_raw_cns(cnsfile))
proteins = collections.defaultdict(list)
rnas = collections.defaultdict(list)
real_cns_items = []
for cnsi in CNS.parse_raw_line(cnsfile):
cns_id = cnsi.cns_id
cns = cnsi.to_dict()
key = (cns['qseqid'], cns['sseqid'])
if cns_id in cpro:
proteins[key].append((cns, cpro[cns_id]))
elif cns_id in crna:
rnas[key].append((cns, crna[cns_id]))
else:
real_cns_items.append((cns_id, cns))
p_trees = fill_tree(proteins)
r_trees = fill_tree(rnas)
def assign_new_names(prs, protein_or_rna):
n = {}
for seqid_pair, li in prs.iteritems():
if not seqid_pair in n: n[seqid_pair] = []
for gnew, info in li[:]:
new_qname = "%(qseqid)s_%(qstart)i_%(qend)i_cns" % gnew
new_sname = "%(sseqid)s_%(sstart)i_%(send)i_cns" % gnew
# and give them both an id so we know they were a pair.
new_qname += "_%s" % (protein_or_rna)
new_sname += "_%s" % (protein_or_rna)
#print >>sys.stderr, gnew['qaccn'], cns["qaccn"]
try:
qstrand = qbed.d[gnew['qaccn']]['strand']
sstrand = sbed.d[gnew['saccn']]['strand']
except:
print >>sys.stderr, gnew
raise
gnew['qaccn'] = new_qname
gnew['saccn'] = new_sname
gnew['qstrand'] = qstrand
gnew['sstrand'] = sstrand
n[seqid_pair].append((gnew, info))
return n
nproteins = assign_new_names(proteins, "protein")
nrnas = assign_new_names(rnas, "rna")
cns_seen = {}
# go through the remaining cnss, print and assign them to the new
# genes (previously cnss) in within dist.
for cns_id, cns in real_cns_items:
print >>real_cns_fh, cns_to_str(cns)
key = (cns['qseqid'], cns['sseqid'])
for pnew, info in get_new(cns, p_trees, key, nproteins, dist + 1000):
cns['qaccn'] = pnew['qaccn']
cns['saccn'] = pnew['saccn']
cns_str = cns_to_str(cns)
if cns_str in cns_seen: continue
cns_seen[cns_str] = 1
print >>real_cns_fh, cns_str
for rnew, info in get_new(cns, r_trees, key, nrnas, dist + 1000):
cns['qaccn'] = rnew['qaccn']
cns['saccn'] = rnew['saccn']
cns_str = cns_to_str(cns)
if cns_str in cns_seen: continue
cns_seen[cns_str] = 1
print >>real_cns_fh, cns_str
qbed_list, qnew_pairs = merge_bed(qbed, nproteins, nrnas, ortho_trees, 'q')
print >> sys.stderr, len(qnew_pairs)
# dont need to do the orthos 2x so send in empty dict.
sbed_list, snew_pairs_unused = merge_bed(sbed, nproteins, nrnas, {}, 's')
# if it's the same org, we add the new cnss again to the same we send in both lists.
# print_bed handles the repeats.
if qbed.path == sbed.path:
qbed_new = sbed_new = print_bed(qbed_list + sbed_list, qbed.path)
else:
qbed_new = print_bed(qbed_list, qbed.path)
sbed_new = print_bed(sbed_list, sbed.path)
return qbed_new.path, sbed_new.path, qnew_pairs
def main(qbed_path, sbed_path, cnsfile, dist, orthology_path):
"""
here, we remove cnss that have been called proteins/rnas from
the cns list, and add them to the bed files.
AND have to do the preliminary assignment of cnss that remain to the new-genes
that _were_ cnss. the proper assignment is then handled in assign.py
"""
qcns_file = qbed_path.replace(".bed", "_cns.gff")
assert qcns_file != qbed_path
qcns_gff = open(qcns_file, 'w')
print >> qcns_gff, "##gff-version 3"
if sbed_path != qbed_path:
scns_file = sbed_path.replace(".bed", "_cns.gff")
assert scns_file != sbed_path
scns_gff = open(scns_file, 'w')
print >> scns_gff, "##gff-version 3"
else:
scns_gff = qcns_gff
qrawbed = RawBed(qbed_path)
srawbed = RawBed(sbed_path)
ortho_trees = read_orthos_to_trees(orthology_path, qrawbed, srawbed)
qbed = Bed(qbed_path)
qbed.fill_dict()
sbed = Bed(sbed_path)
sbed.fill_dict()
name, ext = op.splitext(cnsfile)
real_cns_fh = open("%s.real%s" % (name, ext), "w")
print >> sys.stderr, "writing to:", real_cns_fh.name
outdir = op.dirname(cnsfile)
print >> real_cns_fh, "#qseqid,qaccn,sseqid,saccn,qstart,qend,sstart,send,eval"
crna = read_cns_to_rna(outdir)
cpro = read_cns_to_protein_exons(outdir)
#cns_items = list(parse_raw_cns(cnsfile))
proteins = collections.defaultdict(list)
rnas = collections.defaultdict(list)
real_cns_items = []
for cnsi in CNS.parse_raw_line(cnsfile):
cns_id = cnsi.cns_id
cns = cnsi.to_dict()
key = (cns['qseqid'], cns['sseqid'])
if cns_id in cpro:
proteins[key].append((cns, cpro[cns_id]))
elif cns_id in crna:
rnas[key].append((cns, crna[cns_id]))
else:
real_cns_items.append((cns_id, cns))
p_trees = fill_tree(proteins)
r_trees = fill_tree(rnas)
def assign_new_names(prs, protein_or_rna):
n = {}
for seqid_pair, li in prs.iteritems():
if not seqid_pair in n: n[seqid_pair] = []
for gnew, info in li[:]:
new_qname = "%(qseqid)s_%(qstart)i_%(qend)i_cns" % gnew
new_sname = "%(sseqid)s_%(sstart)i_%(send)i_cns" % gnew
# and give them both an id so we know they were a pair.
new_qname += "_%s" % (protein_or_rna)
new_sname += "_%s" % (protein_or_rna)
#print >>sys.stderr, gnew['qaccn'], cns["qaccn"]
try:
qstrand = qbed.d[gnew['qaccn']]['strand']
sstrand = sbed.d[gnew['saccn']]['strand']
except:
print >> sys.stderr, gnew
raise
gnew['qaccn'] = new_qname
gnew['saccn'] = new_sname
gnew['qstrand'] = qstrand
gnew['sstrand'] = sstrand
n[seqid_pair].append((gnew, info))
return n
nproteins = assign_new_names(proteins, "protein")
nrnas = assign_new_names(rnas, "rna")
cns_seen = {}
# go through the remaining cnss, print and assign them to the new
# genes (previously cnss) in within dist.
for cns_id, cns in real_cns_items:
print >> real_cns_fh, cns_to_str(cns)
key = (cns['qseqid'], cns['sseqid'])
for pnew, info in get_new(cns, p_trees, key, nproteins, dist + 1000):
cns['qaccn'] = pnew['qaccn']
cns['saccn'] = pnew['saccn']
cns_str = cns_to_str(cns)
if cns_str in cns_seen: continue
cns_seen[cns_str] = 1
print >> real_cns_fh, cns_str
for rnew, info in get_new(cns, r_trees, key, nrnas, dist + 1000):
cns['qaccn'] = rnew['qaccn']
cns['saccn'] = rnew['saccn']
cns_str = cns_to_str(cns)
if cns_str in cns_seen: continue
cns_seen[cns_str] = 1
print >> real_cns_fh, cns_str
qbed_list, qnew_pairs = merge_bed(qbed, nproteins, nrnas, ortho_trees, 'q')
print >> sys.stderr, len(qnew_pairs)
# dont need to do the orthos 2x so send in empty dict.
sbed_list, snew_pairs_unused = merge_bed(sbed, nproteins, nrnas, {}, 's')
# if it's the same org, we add the new cnss again to the same we send in both lists.
# print_bed handles the repeats.
if qbed.path == sbed.path:
qbed_new = sbed_new = print_bed(qbed_list + sbed_list, qbed.path)
else:
qbed_new = print_bed(qbed_list, qbed.path)
sbed_new = print_bed(sbed_list, sbed.path)
return qbed_new.path, sbed_new.path, qnew_pairs