def get_sufficient_psi_exons(name, target, sGraph, genome, ID, cutoff, upstream_exon, downstream_exon):
"""
Utilizes the ExonSeek class to find flanking exons that are
good enough to be called "constitutive".
"""
# find appropriate flanking "constitutive" exon for primers
exon_seek_obj = ExonSeek(target, sGraph, ID, cutoff, upstream_exon, downstream_exon)
all_paths, upstream, downstream, component, psi_target, psi_upstream, psi_downstream = exon_seek_obj.get_info()
# lack of successor/predecessor nodes
if upstream is None or downstream is None:
logging.debug("Error: %s does not have an upstream exon, downstream exon, or possibly both" % str(component))
return ["Error: %s does not have an upstream exon, downstream exon, or possibly both" % str(component)]
# get sequence of upstream/target/downstream combo
genome_chr = genome[sGraph.chr] # chr object from pygr
upstream_seq, target_seq, downstream_seq = genome_chr[upstream[0]:upstream[1]], genome_chr[target[0]:target[1]], genome_chr[downstream[0]:downstream[1]] # get sequence using pygr
if sGraph.strand == '-':
upstream_seq, target_seq, downstream_seq = -upstream_seq, -target_seq, -downstream_seq # get reverse-complement if necessary
return [sGraph.strand, name[1:], psi_target,
sGraph.chr + ':' + '-'.join(map(str, upstream)), # upstream eg. +chr1:1000-2000
psi_upstream,
sGraph.chr + ':' + '-'.join(map(str, downstream)), # downstream eg. +chr1:1000-2000
psi_downstream,
all_paths, upstream_seq,
target_seq, downstream_seq]
def get_sufficient_psi_exons(name, target, sGraph, genome, ID, cutoff,
upstream_exon, downstream_exon):
"""
Utilizes the ExonSeek class to find flanking exons that are
good enough to be called "constitutive".
"""
# find appropriate flanking "constitutive" exon for primers
exon_seek_obj = ExonSeek(target, sGraph, ID, cutoff, upstream_exon,
downstream_exon)
all_paths, upstream, downstream, component, psi_target, psi_upstream, psi_downstream = exon_seek_obj.get_info(
)
# lack of successor/predecessor nodes
if upstream is None or downstream is None:
logging.debug(
"Error: %s does not have an upstream exon, downstream exon, or possibly both"
% str(component))
return [
"Error: %s does not have an upstream exon, downstream exon, or possibly both"
% str(component)
]
# get sequence of upstream/target/downstream combo
genome_chr = genome[sGraph.chr] # chr object from pygr
upstream_seq, target_seq, downstream_seq = genome_chr[
upstream[0]:upstream[1]], genome_chr[target[0]:target[1]], genome_chr[
downstream[0]:downstream[1]] # get sequence using pygr
if sGraph.strand == '-':
upstream_seq, target_seq, downstream_seq = -upstream_seq, -target_seq, -downstream_seq # get reverse-complement if necessary
return [
sGraph.strand,
name[1:],
psi_target,
sGraph.chr + ':' +
'-'.join(map(str, upstream)), # upstream eg. +chr1:1000-2000
psi_upstream,
sGraph.chr + ':' +
'-'.join(map(str, downstream)), # downstream eg. +chr1:1000-2000
psi_downstream,
all_paths,
upstream_seq,
target_seq,
downstream_seq
]
def primerseq_defined_exons(tmp_sg, line, psi_option):
"""
Get information about counts and paths if using PrimerSeq to define the flanking exons.
"""
# not the best use of the ExonSeek object, initially intended to find appropriate flanking exons
# but in this case ExonSeek is used to get the transcripts and associate counts
ID = line[utils.ID]
tgt_pos = utils.get_pos(line[utils.TARGET])
exon_seek_obj = ExonSeek(
tgt_pos,
tmp_sg,
ID,
psi_option,
None, # no defined upstream exon
None) # no defined downstream exon
all_paths, upstream, downstream, component, psi_target, psi_upstream, psi_downstream = exon_seek_obj.get_info(
)
return exon_seek_obj.paths, exon_seek_obj.counts
def primerseq_defined_exons(tmp_sg, line, psi_option):
"""
Get information about counts and paths if using PrimerSeq to define the flanking exons.
"""
# not the best use of the ExonSeek object, initially intended to find appropriate flanking exons
# but in this case ExonSeek is used to get the transcripts and associate counts
ID = line[utils.ID]
tgt_pos = utils.get_pos(line[utils.TARGET])
exon_seek_obj = ExonSeek(tgt_pos,
tmp_sg,
ID,
psi_option,
None, # no defined upstream exon
None) # no defined downstream exon
all_paths, upstream, downstream, component, psi_target, psi_upstream, psi_downstream = exon_seek_obj.get_info()
return exon_seek_obj.paths, exon_seek_obj.counts