"""
Utilities for working with GFF3 files.
"""
from petl.io import fromtsv
from petl.transform import skipcomments, rowlenselect, convert, pushheader
from urllib import unquote_plus
from petl.util import HybridRow, RowContainer
from petlx.interval import facetintervallookup, intervaljoin, intervalleftjoin
import sys
def gff3_parse_attributes(attributes_string):
"""
Parse a string of GFF3 attributes ('key=value' pairs delimited by ';')
and return a dictionary.
.. versionadded:: 0.2
"""
attributes = dict()
fields = attributes_string.split(';')
for f in fields:
if '=' in f:
key, value = f.split('=')
attributes[unquote_plus(key).strip()] = unquote_plus(value.strip())
elif len(f) > 0:
# not strictly kosher
attributes[unquote_plus(f).strip()] = True
return attributes
[docs]def fromgff3(filename):
"""
Extract feature rows from a GFF3 file.
.. versionadded:: 0.2
"""
# parse file as tab-delimited
t0 = fromtsv(filename)
# push header
t1 = pushheader(t0, ('seqid', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase', 'attributes'))
# skip comments
t2 = skipcomments(t1, '#')
# ignore any row not 9 values long (e.g., trailing fasta)
t3 = rowlenselect(t2, 9)
# parse attributes into a dict
t4 = convert(t3, 'attributes', gff3_parse_attributes)
# parse coordinates
t5 = convert(t4, ('start', 'end'), int)
return HybridRowView(t5)
# TODO move this to petl.base?
class HybridRowView(RowContainer):
def __init__(self, wrapped):
self.wrapped = wrapped
def cachetag(self):
return self.wrapped.cachetag()
def __iter__(self):
it = iter(self.wrapped)
fields = it.next()
yield fields
for row in it:
yield HybridRow(row, fields, missing=None)
[docs]def gff3lookup(features, facet='seqid'):
"""
Build a GFF3 feature lookup based on interval trees. See also
:func:`petlx.interval.facetintervallookup`.
.. versionadded:: 0.2
"""
return facetintervallookup(features, facet=facet, start='start', stop='end')
[docs]def gff3join(table, features, seqid='seqid', start='start', end='end', proximity=1):
"""
Join with a table of GFF3 features. See also :func:`petlx.interval.intervaljoin`.
.. versionadded:: 0.2
"""
return intervaljoin(table, features, lstart=start, lstop=end, lfacet=seqid,
rstart='start', rstop='end', rfacet='seqid',
proximity=proximity)
[docs]def gff3leftjoin(table, features, seqid='seqid', start='start', end='end', proximity=1):
"""
Left join with a table of GFF3 features. See also :func:`petlx.interval.intervalleftjoin`.
.. versionadded:: 0.2
"""
return intervalleftjoin(table, features, lstart=start, lstop=end, lfacet=seqid,
rstart='start', rstop='end', rfacet='seqid',
proximity=proximity)
from petlx.integration import integrate
integrate(sys.modules[__name__])