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"""
Conversion functions that operate on :class:`FeatureDB` classes.
"""
import six
def to_bed12(f, db, child_type='exon', name_field='ID'):
"""
Given a top-level feature (e.g., transcript), construct a BED12 entry
Parameters
----------
f : Feature object or string
This is the top-level feature represented by one BED12 line. For
a canonical GFF or GTF, this will generally be a transcript.
db : a FeatureDB object
This is need to get the children for the feature
child_type : str
Featuretypes that will be represented by the BED12 "blocks". Typically
"exon".
name_field : str
Attribute to be used in the "name" field of the BED12 entry. Usually
"ID" for GFF; "transcript_id" for GTF.
"""
if isinstance(f, six.string_types):
f = db[f]
children = list(db.children(f, featuretype=child_type, order_by='start'))
sizes = [len(i) for i in children]
starts = [i.start - f.start for i in children]
fields = [
f.chrom,
f.start - 1, # GTF -> BED coord system
f.stop,
f.attributes.get(name_field, ['.'])[0],
f.score,
f.strand,
f.start,
f.stop,
'0,0,0',
len(children),
','.join(map(str, sizes)),
','.join(map(str, starts))
]
return '\t'.join(map(str, fields)) + '\n'
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