def extract_seq(contig, strand, ref_clv, ref_fa, ctg_clv, window=50):
"""
extract the upstream sequence for PAS hexamer search
:param ref_clv: would be necessary needs to combine sequence from both
contig and reference genome
:param ctg_clv: the position of clv in contig coordinate.
"""
seqname = contig.reference_name
# TODO: this can be done in one step, but needs update a lot of tests
if apautils.is_hardclipped(contig):
ctg_seq = apautils.infer_query_sequence(contig, always=True)
else:
ctg_seq = contig.query_sequence
cigartuples = contig.cigartuples
args = cigartuples, ctg_seq, seqname, strand, ctg_clv, ref_clv, ref_fa, window
if strand == '+':
return xseq_plus.extract(*args)
elif strand == '-':
return xseq_minus.extract(*args)
else:
raise ValueError('unknown strand: "{0}"'.format(strand))
def gen_clv_record(contig, r2c_bam, tail_side, ref_fa):
"""
:param contig: suffix contig
:param r2c_bam: pysam instance of read2genome alignment BAM
:param tail_side (TODO, rename to tail_direction): 'left' or 'right'
:param ref_fa: pysam instance of reference genome fasta. if provided,
will also search PAS hexamer on reference genome.
"""
strand = calc_strand(tail_side)
ref_clv = calc_ref_clv(contig, tail_side)
ctg_tail_len = apautils.calc_tail_length(contig, tail_side)
ctg_seq_len = contig.infer_query_length(always=True)
ctg_clv = calc_ctg_clv(strand, ctg_seq_len, ctg_tail_len)
num_suffix_reads, max_suffix_read_tail_len = analyze_suffix_reads(
r2c_bam, contig, ctg_clv)
ctg_hex, ctg_hex_id, ctg_hex_pos = gen_contig_hexamer_tuple(
contig, strand, ref_clv, ref_fa, ctg_clv)
ref_hex, ref_hex_id, ref_hex_pos = gen_reference_hexamer_tuple(
ref_fa, contig.reference_name, strand, ref_clv)
return ClvRecord(
contig.reference_name,
strand,
ref_clv,
ctg_hex,
ctg_hex_id,
ctg_hex_pos,
ref_hex,
ref_hex_id,
ref_hex_pos,
evidence_type='suffix',
contig_id_at_pos='{0}@{1}'.format(contig.query_name, ctg_clv),
contig_len=contig.query_length,
contig_mapq=contig.mapq,
contig_is_hardclipped=apautils.is_hardclipped(contig),
num_suffix_reads=num_suffix_reads,
max_suffix_read_tail_len=max_suffix_read_tail_len,
suffix_contig_tail_len=ctg_tail_len,
num_suffix_contigs=1,
num_bridge_reads=0,
max_bridge_read_tail_len=0,
num_bridge_contigs=0,
num_link_reads=0,
num_link_contigs=0,
num_blank_contigs=0,
)
def gen_clv_record(contig, clv_key_tuple, num_link_reads, ref_fa):
"""
:param contig: link contig
:clv_key_tuple: a tuple of (seqname, strand, cleavage_site_position)
:param ref_fa: if provided, search PAS hexamer on reference genome, too
"""
seqname, strand, ref_clv = clv_key_tuple
ctg_seq_len = contig.infer_query_length(always=True)
ctg_clv = calc_ctg_clv(strand, ctg_seq_len)
ctg_hex, ctg_hex_id, ctg_hex_pos = gen_contig_hexamer_tuple(
contig, strand, ref_clv, ref_fa, ctg_clv)
ref_hex, ref_hex_id, ref_hex_pos = gen_reference_hexamer_tuple(
ref_fa, contig.reference_name, strand, ref_clv)
return ClvRecord(
seqname,
strand,
ref_clv,
ctg_hex,
ctg_hex_id,
ctg_hex_pos,
ref_hex,
ref_hex_id,
ref_hex_pos,
evidence_type='link',
contig_id_at_pos='{0}@{1}'.format(contig.query_name, ctg_clv),
contig_len=contig.query_length,
contig_mapq=contig.mapq,
contig_is_hardclipped=apautils.is_hardclipped(contig),
num_suffix_reads=0,
max_suffix_read_tail_len=0,
suffix_contig_tail_len=0,
num_suffix_contigs=0,
num_bridge_reads=0,
max_bridge_read_tail_len=0,
num_bridge_contigs=0,
num_link_reads=num_link_reads,
num_link_contigs=1,
num_blank_contigs=0,
)
def gen_two_clv_records(contig, ref_fa, already_supported_clv_keys):
"""
Assume there is still a clv at the 3' end of the contig even without any
polya evidence, in thus case, there is no direction, so either end of the
contig could be a clv. Hence add two to the function name explicitly
"""
seqname = contig.reference_name
strands = ['+', '-']
ref_clv_candidates = [
contig.reference_end - 1,
contig.reference_start
]
is_hardclipped = apautils.is_hardclipped(contig)
for strand, ref_clv in zip(strands, ref_clv_candidates):
clv_key = apautils.gen_clv_key_tuple(seqname, strand, ref_clv)
if clv_key in already_supported_clv_keys:
continue
ctg_seq_len = contig.infer_query_length(always=True)
ctg_clv = calc_ctg_clv(strand, ctg_seq_len)
ctg_hex, ctg_hex_id, ctg_hex_pos = gen_contig_hexamer_tuple(
contig, strand, ref_clv, ref_fa, ctg_clv)
ref_hex, ref_hex_id, ref_hex_pos = gen_reference_hexamer_tuple(
ref_fa, contig.reference_name, strand, ref_clv)
yield ClvRecord(
contig.reference_name,
strand,
ref_clv,
ctg_hex,
ctg_hex_id,
ctg_hex_pos,
ref_hex,
ref_hex_id,
ref_hex_pos,
evidence_type='blank',
contig_id_at_pos='{0}@{1}'.format(contig.query_name, ctg_clv),
contig_len=contig.query_length,
contig_mapq=contig.mapq,
contig_is_hardclipped=is_hardclipped,
num_suffix_reads=0,
max_suffix_read_tail_len=0,
suffix_contig_tail_len=0,
num_suffix_contigs=0,
num_bridge_reads=0,
max_bridge_read_tail_len=0,
num_bridge_contigs=0,
num_link_reads=0,
num_link_contigs=0,
num_blank_contigs=1,
)