def make_seq_record(exon, skip_annotation=False):
""" use pycogent to grab the sequence for the exon's region, and create a
new seq record with all the bells and whistles. add in the predicted
exon start and ends and splice sites as well.
"""
# GET SEQ FROM PYCOGENT
# ===========================================================================
cog_reg = hs37.getRegion(CoordName=exon["chr"], Start=exon["synth_start"] - 1, End=exon["synth_end"])
cog_seq = cog_reg.Seq
# reverse complement if necessary
if exon["strand"] == -1:
cog_seq = cog_seq.rc()
seq = cog_seq._seq
if not skip_annotation:
# DO SNPS
# ===========================================================================
var = hs37.getFeatures(feature_types="variation", region=cog_reg)
exon["snps"] = []
for snp in var:
if snp.Alleles != "HGMD_MUTATION":
exon["snps"].append(snp)
# TODO: APPEND OUTER INTRON CONTEXT
# ===========================================================================
# use the cfg information to get sequence, how much to add
# MAKE SEQ RECORD
# ===========================================================================
# create the seqRecord object, adding the exon dict as annotation fields
record = SeqRecord(Seq(seq, generic_dna), id=exon["exon"], annotations=exon)
# add the exon features and putative splicing features, set the source as
# ensembl_exon (not splicemod, so that it doesn't get deleted)
if exon["strand"] == 1:
in_front = exon["synth_us"]
else:
in_front = exon["synth_ds"]
record.features = [
SeqFeature(FeatureLocation(in_front, (exon["len"] + in_front)), type="exon"),
SeqFeature(FeatureLocation(0, in_front), type="intron"),
SeqFeature(FeatureLocation(in_front + exon["len"], len(seq)), type="intron"),
]
for feat in record.features:
feat.qualifiers["source"] = "ensembl_exon"
record.description = (
"{r.id} chr{chr}:{synth_start}-{synth_end} "
+ "strand={strand} len={synth_us}.{len}.{synth_ds} "
+ "ccds={CCDS}"
).format(r=record, **record.annotations)
if not skip_annotation:
record.populate_attribs()
add_wiggle_data(record)
record.add_conservation_features()
return record
