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 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 writeBed(self, genome, detailsFields, classifyFields, classifyValues, classifyOperations, categoryName):
bedPath = os.path.join(self.bedDir, categoryName, genome, genome + ".bed")
with open(bedPath, "w") as outf:
for details in detailsFields:
for record in sql_lib.selectBetweenDatabases(self.cur, "details", details, classifyFields, classifyValues, classifyOperations, self.primaryKeyColumn, genome):
if record[0] == None:
continue
elif type(record[0]) == type(u''):
outf.write(record[0] + "\n")
else:
for x in record[0]:
outf.write(x)
return bedPath
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 writeBed(self, genome, detailsFields, classifyFields, classifyValues,
classifyOperations, categoryName):
bedPath = os.path.join(self.bedDir, categoryName, genome,
genome + ".bed")
with open(bedPath, "w") as outf:
for details in detailsFields:
for record in sql_lib.selectBetweenDatabases(
self.cur, "details", details, classifyFields,
classifyValues, classifyOperations,
self.primaryKeyColumn, genome):
if record[0] == None:
continue
elif type(record[0]) == type(u''):
outf.write(record[0] + "\n")
else:
for x in record[0]:
outf.write(x)
return bedPath
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]
