def import_external_fasta(input_file):
"""
Create a FastaGenome object, set its metadata, and populate it with the
data from a fasta file.
Must return the data as the single item in an array, because other file
formats potentially contain several genomes.
"""
from nasp.nasp_objects import FastaGenome
genome = FastaGenome()
set_genome_metadata(genome, input_file)
genome.import_fasta_file(genome.file_path(), "franken::")
# from sys import stdout
#genome._genome._send_to_fasta_handle( stdout )
return [genome]
def setUp(self):
reference_path = testdata.REFERENCE_FASTA
dups_path = testdata.REFERENCE_DUPS
reference = ReferenceGenome()
reference.import_fasta_file(reference_path)
reference.import_dups_file(dups_path)
self.genome = GenomeCollection()
fasta = FastaGenome()
fasta.import_fasta_file(reference_path)
self.genome.add_genome(fasta)
self.genome.set_reference(reference)
# Statistics are gathered when the matrices are created
self.genome.write_to_matrices({})
self.tmpfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
def import_external_fasta(input_file):
"""
Create a FastaGenome object, set its metadata, and populate it with the
data from a fasta file.
Must return the data as the single item in an array, because other file
formats potentially contain several genomes.
"""
from nasp.nasp_objects import FastaGenome
genome = FastaGenome()
set_genome_metadata(genome, input_file)
genome.import_fasta_file(genome.file_path(), "franken::")
# from sys import stdout
#genome._genome._send_to_fasta_handle( stdout )
return [genome]
def setUp(self):
reference_path = testdata.REFERENCE_FASTA
dups_path = testdata.REFERENCE_DUPS
reference = ReferenceGenome()
reference.import_fasta_file(reference_path)
reference.import_dups_file(dups_path)
self.genome = GenomeCollection()
fasta = FastaGenome()
fasta.import_fasta_file(reference_path)
self.genome.add_genome(fasta)
self.genome.set_reference(reference)
self.tmpfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
self.matrix_formats = [
{
'dataformat': 'matrix',
'handle': self.tmpfile,
'filter': ''
}
]
