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src/b/c/bcbb-HEAD/gff/Scripts/gff/gff2_to_gff3.py   bcbb(Download)
import os
 
from BCBio.GFF import GFFParser, GFF3Writer
 
def main(in_file):
    base, ext = os.path.splitext(in_file)
    out_file = "%s.gff3" % (base)
    in_handle = open(in_file)
    out_handle = open(out_file, "w")
    reader = GFFParser()

src/b/c/bcbb-HEAD/gff/Scripts/gff/access_gff_index.py   bcbb(Download)
    def __init__(self, *args, **kwargs):
        interval_index_file.AbstractIndexedAccess.__init__(self, *args,
                **kwargs)
        self._parser = GFF.GFFParser()
 

src/b/c/bcbb-HEAD/gff/Scripts/gff/gff_to_biosql.py   bcbb(Download)
from Bio import SeqIO
 
from BCBio.GFF import GFFParser
 
def main(seq_file, gff_file):
 
    print "Parsing GFF data file..."
    parser = GFFParser()
    recs = parser.parse(gff_file, seq_dict, limit_info=limit_info)
 

src/b/c/bcbb-HEAD/gff/Tests/test_GFFSeqIOFeatureAdder.py   bcbb(Download)
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
from BCBio.GFF import (GFFExaminer, GFFParser, DiscoGFFParser)
 
class MapReduceGFFTest(unittest.TestCase):
                         ('Promoterome', 'PCR_product')]
            )
        parser = GFFParser()
        rec_dict = SeqIO.to_dict(parser.parse(self._test_gff_file, seq_dict,
            limit_info=pcr_limit_info))
                gff_id = ['I']
                )
        parser = GFFParser()
        rec_dict = SeqIO.to_dict(parser.parse(self._test_gff_file, seq_dict,
            limit_info=cds_limit_info))
                gff_id = ['I']
                )
        parser = GFFParser()
        rec_dict = SeqIO.to_dict(parser.parse(self._test_gff_file, seq_dict,
            limit_info=cds_limit_info))
    def t_no_dict_error(self):
        """Ensure an error is raised when no dictionary to map to is present.
        """
        parser = GFFParser(create_missing=False)
        try: