def add_sample(self, gff_filename, group_filename, sample_prefix, output_prefix, fastq_filename=None):
combined = [] # list of (r1 if r2 is None | r2 if r1 is None | longer of r1 or r2 if both not None)
unmatched_recs = self.record_d_fusion.keys()
for _id, records in GFF.collapseGFFFusionReader(gff_filename):
match_seqid = self.match_fusion_record(records)
if match_seqid is not None:
combined.append((self.record_d_fusion[match_seqid], records))
try:
unmatched_recs.remove(match_seqid)
except ValueError:
pass # already deleted, OK, this happens for single-exon transcripts
else: # r is not present in current tree
combined.append((None, records))
# put whatever is left from the tree in
for seqid in unmatched_recs:
combined.append((self.record_d_fusion[seqid], None))
#return combined
# create a ClusterTree to re-calc the loci/transcripts
final_tree = defaultdict(lambda: {'+': ClusterTree(0, 0), '-':ClusterTree(0, 0)})
for i,(r1s,r2s) in enumerate(combined):
if r2s is None or (r1s is not None and r1s[0].end-r1s[0].start > r2s[0].end-r2s[0].start):
final_tree[r1s[0].chr][r1s[0].strand].insert(r1s[0].start, r1s[0].end, i)
else:
final_tree[r2s[0].chr][r2s[0].strand].insert(r2s[0].start, r2s[0].end, i)
self.write_cluster_tree_as_gff(final_tree, combined, group_filename, sample_prefix, output_prefix, fastq_filename2=fastq_filename)
def add_sample(self, gff_filename, group_filename, sample_prefix, output_prefix, fastq_filename=None):
combined = [] # list of (r1 if r2 is None | r2 if r1 is None | longer of r1 or r2 if both not None)
unmatched_recs = list(self.record_d_fusion.keys())
for _id, records in GFF.collapseGFFFusionReader(gff_filename):
match_seqid = self.match_fusion_record(records)
if match_seqid is not None:
combined.append((self.record_d_fusion[match_seqid], records))
try:
unmatched_recs.remove(match_seqid)
except ValueError:
pass # already deleted, OK, this happens for single-exon transcripts
else: # r is not present in current tree
combined.append((None, records))
# put whatever is left from the tree in
for seqid in unmatched_recs:
combined.append((self.record_d_fusion[seqid], None))
# create a ClusterTree to re-calc the loci/transcripts
final_tree = defaultdict(lambda: {'+': ClusterTree(0, 0), '-':ClusterTree(0, 0)})
for i,(r1s,r2s) in enumerate(combined):
if r2s is None or (r1s is not None and r1s[0].end-r1s[0].start > r2s[0].end-r2s[0].start):
final_tree[r1s[0].chr][r1s[0].strand].insert(r1s[0].start, r1s[0].end, i)
else:
final_tree[r2s[0].chr][r2s[0].strand].insert(r2s[0].start, r2s[0].end, i)
self.write_cluster_tree_as_gff(final_tree, combined, group_filename, sample_prefix, output_prefix, fastq_filename2=fastq_filename)
def sample_sanity_check(group_filename,
gff_filename,
count_filename,
fastq_filename=None):
"""
Double check that the formats are expected and all PBIDs are concordant across the files
:return: raise Exception if sanity check failed
"""
print >> sys.stderr, "Sanity checking. Retrieving PBIDs from {0},{1},{2}...".format(\
group_filename, gff_filename, count_filename)
ids1 = [line.strip().split()[0] for line in open(group_filename)]
ids2 = [
fusion_id
for fusion_id, rs in GFF.collapseGFFFusionReader(gff_filename)
]
f = open(count_filename)
for i in xrange(14):
f.readline() # just through the header
ids3 = [r['pbid'] for r in DictReader(f, delimiter='\t')]
if len(set(ids2).difference(ids1)) > 0 or len(
set(ids2).difference(ids3)) > 0:
raise Exception, "Sanity check failed! Please make sure the PBIDs listed in {1} are also in {0} and {2}".format(\
group_filename, gff_filename, count_filename)
if fastq_filename is not None:
ids4 = [
r.id.split('|')[0]
for r in SeqIO.parse(open(fastq_filename), 'fastq')
]
if len(set(ids2).difference(ids4)) > 0:
raise Exception, "Sanity check failed! Please make sure the PBIDs listed in {1} are also in {0}".format(\
fastq_filename, gff_filename)
def __init__(self, gff_filename, group_filename, internal_fuzzy_max_dist=0, self_prefix=None, fastq_filename=None, fusion_max_dist=10):
"""
Differences with non-fusion MegaPBTree:
1. allow_5merge is always FALSE. Not a parameter.
2. fusion_max_dist --- maximum allowed distance on internal fusion sites to be called as equivalent fusions
"""
super(MegaPBTreeFusion, self).__init__(gff_filename, group_filename, internal_fuzzy_max_dist, self_prefix, False, fastq_filename)
self.fusion_max_dist = fusion_max_dist
# ex: PBfusion.1 -> [PBfusion.1.1, PBfusion.1.2]
self.record_d_fusion = dict((fusion_id, records) for fusion_id,records in GFF.collapseGFFFusionReader(gff_filename))
def __init__(self, gff_filename, group_filename, internal_fuzzy_max_dist=0, self_prefix=None, fastq_filename=None, fusion_max_dist=10):
"""
Differences with non-fusion MegaPBTree:
1. allow_5merge is always FALSE. Not a parameter.
2. fusion_max_dist --- maximum allowed distance on internal fusion sites to be called as equivalent fusions
"""
super(MegaPBTreeFusion, self).__init__(gff_filename, group_filename, internal_fuzzy_max_dist, self_prefix, False, fastq_filename)
self.fusion_max_dist = fusion_max_dist
# ex: PBfusion.1 -> [PBfusion.1.1, PBfusion.1.2]
self.record_d_fusion = dict((fusion_id, records) for fusion_id,records in GFF.collapseGFFFusionReader(gff_filename))
def sample_sanity_check(group_filename, gff_filename, count_filename, fastq_filename=None):
"""
Double check that the formats are expected and all PBIDs are concordant across the files
:return: raise Exception if sanity check failed
"""
print >> sys.stderr, "Sanity checking. Retrieving PBIDs from {0},{1},{2}...".format(\
group_filename, gff_filename, count_filename)
ids1 = [line.strip().split()[0] for line in open(group_filename)]
ids2 = [fusion_id for fusion_id,rs in GFF.collapseGFFFusionReader(gff_filename)]
f = open(count_filename)
for i in xrange(14): f.readline() # just through the header
ids3 = [r['pbid'] for r in DictReader(f, delimiter='\t')]
if len(set(ids2).difference(ids1))>0 or len(set(ids2).difference(ids3))>0:
raise Exception, "Sanity check failed! Please make sure the PBIDs listed in {1} are also in {0} and {2}".format(\
group_filename, gff_filename, count_filename)
if fastq_filename is not None:
ids4 = [r.id.split('|')[0] for r in SeqIO.parse(open(fastq_filename), 'fastq')]
if len(set(ids2).difference(ids4))>0:
raise Exception, "Sanity check failed! Please make sure the PBIDs listed in {1} are also in {0}".format(\
fastq_filename, gff_filename)
def sample_sanity_check(group_filename,
gff_filename,
count_filename,
fastq_filename=None):
"""
Double check that the formats are expected and all PBIDs are concordant across the files
:return: raise Exception if sanity check failed
"""
print("Sanity checking. Retrieving PBIDs from {0},{1},{2}...".format(\
group_filename, gff_filename, count_filename), file=sys.stderr)
ids1 = [line.strip().split()[0] for line in open(group_filename)]
ids2 = [
fusion_id
for fusion_id, rs in GFF.collapseGFFFusionReader(gff_filename)
]
f = open(count_filename)
while True:
# advance through the headers which start with #
cur = f.tell()
if not f.readline().startswith('#') or f.tell(
) == cur: # first non-# seen or EOF
f.seek(cur)
break
ids3 = [r['pbid'] for r in DictReader(f, delimiter='\t')]
if len(set(ids2).difference(ids1)) > 0 or len(
set(ids2).difference(ids3)) > 0:
raise Exception("Sanity check failed! Please make sure the PBIDs listed in {1} are also in {0} and {2}".format(\
group_filename, gff_filename, count_filename))
if fastq_filename is not None:
ids4 = [
r.id.split('|')[0]
for r in SeqIO.parse(open(fastq_filename), 'fastq')
]
if len(set(ids2).difference(ids4)) > 0:
raise Exception("Sanity check failed! Please make sure the PBIDs listed in {1} are also in {0}".format(\
fastq_filename, gff_filename))
