def recolorTransMap(self, genome, gp):
"""
Recolors the comparativeAnnotation results based on the scheme assembly > alignment > biology. Transcripts not in
one of these categories will become black.
"""
records = seq_lib.get_gene_pred_transcripts(gp)
# first we recolor everything black
for x in records:
x.rgb = "0"
# now we find all interesting biology and color that the interesting biology color
detailsFields, classifyFields, classifyValues, classifyOperations = src.queries.interestingBiology()
aIds = {x[0] for x in sql_lib.selectBetweenDatabases(self.cur, "details", self.primaryKeyColumn, classifyFields, classifyValues, classifyOperations, self.primaryKeyColumn, genome)}
for x in records:
if x.name in aIds:
x.rgb = self.colors["mutation"]
# now the alignment errors...
detailsFields, classifyFields, classifyValues, classifyOperations = src.queries.alignmentErrors()
aIds = {x[0] for x in sql_lib.selectBetweenDatabases(self.cur, "details", self.primaryKeyColumn, classifyFields, classifyValues, classifyOperations, self.primaryKeyColumn, genome)}
for x in records:
if x.name in aIds:
x.rgb = self.colors["alignment"]
# finally the assembly
detailsFields, classifyFields, classifyValues, classifyOperations = src.queries.assemblyErrors()
aIds = {x[0] for x in sql_lib.selectBetweenDatabases(self.cur, "details", self.primaryKeyColumn, classifyFields, classifyValues, classifyOperations, self.primaryKeyColumn, genome)}
for x in records:
if x.name in aIds:
x.rgb = self.colors["assembly"]
return ["\t".join(map(str, x.get_bed())) for x in records]
def get_transcript_dict(gp, filter_set):
transcripts = seq_lib.get_gene_pred_transcripts(gp)
d = seq_lib.transcript_list_to_dict(transcripts, noDuplicates=True)
r = defaultdict(list)
for aln_id, rec in d.iteritems():
tx_id = strip_alignment_numbers(aln_id)
if tx_id in filter_set:
r[tx_id].append(rec)
return r
def get_transcript_dict(gp, filter_set):
transcripts = seq_lib.get_gene_pred_transcripts(gp)
d = seq_lib.transcript_list_to_dict(transcripts, noDuplicates=True)
r = defaultdict(list)
for aln_id, rec in d.iteritems():
tx_id = strip_alignment_numbers(aln_id)
if tx_id in filter_set:
r[tx_id].append(rec)
return r
def recolorAugustus(self, genome, gp):
"""
Recolors the Augustus tracks based on OK-ness.
"""
records = seq_lib.get_gene_pred_transcripts(gp)
# first we recolor everything black
for x in records:
x.rgb = "0"
detailsFields, classifyFields, classifyValues, classifyOperations = src.augustusQueries.augustusNotOk()
aIds = {x[0] for x in sql_lib.selectBetweenDatabases(self.cur, "details", self.primaryKeyColumn, classifyFields, classifyValues, classifyOperations, self.primaryKeyColumn, genome)}
for x in records:
if x.name in aIds:
x.rgb = "83,179,64"
return ["\t".join(map(str, x.get_bed())) for x in records]
def recolorTransMap(self, genome, gp):
"""
Recolors the comparativeAnnotation results based on the scheme assembly > alignment > biology. Transcripts not in
one of these categories will become black.
"""
records = seq_lib.get_gene_pred_transcripts(gp)
# first we recolor everything black
for x in records:
x.rgb = "0"
# now we find all interesting biology and color that the interesting biology color
detailsFields, classifyFields, classifyValues, classifyOperations = src.queries.interestingBiology(
)
aIds = {
x[0]
for x in sql_lib.selectBetweenDatabases(
self.cur, "details", self.primaryKeyColumn, classifyFields,
classifyValues, classifyOperations, self.primaryKeyColumn,
genome)
}
for x in records:
if x.name in aIds:
x.rgb = self.colors["mutation"]
# now the alignment errors...
detailsFields, classifyFields, classifyValues, classifyOperations = src.queries.alignmentErrors(
)
aIds = {
x[0]
for x in sql_lib.selectBetweenDatabases(
self.cur, "details", self.primaryKeyColumn, classifyFields,
classifyValues, classifyOperations, self.primaryKeyColumn,
genome)
}
for x in records:
if x.name in aIds:
x.rgb = self.colors["alignment"]
# finally the assembly
detailsFields, classifyFields, classifyValues, classifyOperations = src.queries.assemblyErrors(
)
aIds = {
x[0]
for x in sql_lib.selectBetweenDatabases(
self.cur, "details", self.primaryKeyColumn, classifyFields,
classifyValues, classifyOperations, self.primaryKeyColumn,
genome)
}
for x in records:
if x.name in aIds:
x.rgb = self.colors["assembly"]
return ["\t".join(map(str, x.get_bed())) for x in records]
def recolorAugustus(self, genome, gp):
"""
Recolors the Augustus tracks based on OK-ness.
"""
records = seq_lib.get_gene_pred_transcripts(gp)
# first we recolor everything black
for x in records:
x.rgb = "0"
detailsFields, classifyFields, classifyValues, classifyOperations = src.augustusQueries.augustusNotOk(
)
aIds = {
x[0]
for x in sql_lib.selectBetweenDatabases(
self.cur, "details", self.primaryKeyColumn, classifyFields,
classifyValues, classifyOperations, self.primaryKeyColumn,
genome)
}
for x in records:
if x.name in aIds:
x.rgb = "83,179,64"
return ["\t".join(map(str, x.get_bed())) for x in records]
def load_gp(path):
tm_recs = seq_lib.get_gene_pred_transcripts(path)
tm_dict = seq_lib.transcript_list_to_dict(tm_recs, noDuplicates=True)
return tm_dict
def load_gp(path):
tm_recs = seq_lib.get_gene_pred_transcripts(path)
tm_dict = seq_lib.transcript_list_to_dict(tm_recs, noDuplicates=True)
return tm_dict