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src/b/c/bcbb-HEAD/gff/Scripts/gff/gff_to_biosql.py   bcbb(Download)
    print "Parsing GFF data file..."
    parser = GFFParser()
    recs = parser.parse(gff_file, seq_dict, limit_info=limit_info)
 
    print "Writing to BioSQL database..."

src/b/c/bcbb-HEAD/gff/BCBio/GFF/__init__.py   bcbb(Download)
"""Top level of GFF parsing providing shortcuts for useful classes.
"""
from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple
from BCBio.GFF.GFFOutput import GFF3Writer, write
 

src/b/c/bcbio-gff-0.4/BCBio/GFF/__init__.py   bcbio-gff(Download)
"""Top level of GFF parsing providing shortcuts for useful classes.
"""
from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple
from BCBio.GFF.GFFOutput import GFF3Writer, write
 

src/b/c/bcbb-HEAD/gff/Tests/test_GFFSeqIOFeatureAdder.py   bcbb(Download)
            )
        parser = GFFParser()
        rec_dict = SeqIO.to_dict(parser.parse(self._test_gff_file, seq_dict,
            limit_info=pcr_limit_info))
        assert len(rec_dict['I'].features) == 4
                )
        parser = GFFParser()
        rec_dict = SeqIO.to_dict(parser.parse(self._test_gff_file, seq_dict,
            limit_info=cds_limit_info))
        final_rec = rec_dict['I']
                )
        parser = GFFParser()
        rec_dict = SeqIO.to_dict(parser.parse(self._test_gff_file, seq_dict,
            limit_info=cds_limit_info))
        final_rec = rec_dict['I']
        parser = GFFParser(create_missing=False)
        try:
            for rec in parser.parse(self._test_gff_file):
                pass
            # no error -- problem
    def t_gff_annotations(self):
        """Check GFF annotations placed on an entire sequence.
        """
        parser = GFFParser()
        rec_dict = SeqIO.to_dict(parser.parse(self._test_gff_ann_file))