Python run_quast Beispiele

Beispiel #1

Datei: test_genes_txt.py Projekt: ctb/quast

#!/usr/bin/python

import os
from common import run_quast, contigs_1k_2, reference_1k, assert_metric

name = os.path.basename(__file__)[5:-3]


run_quast(name, contigs=[contigs_1k_2], params='-R ' + reference_1k + ' -G genes_1k.txt')
assert_metric(name, '# genes', ['1 + 1 part'])

Beispiel #2

Datei: test_genes_gff.py Projekt: ctb/quast

#!/usr/bin/python

import os
from common import run_quast, contigs_1k_2, reference_1k, assert_metric

name = os.path.basename(__file__)[5:-3]


run_quast(name, contigs=[contigs_1k_2], params='-R ' + reference_1k + ' -G genes_1k_simple.gff')
assert_metric(name, '# genes', ['1 + 1 part'])

Beispiel #3

Datei: test_reference.py Projekt: svpipaliya/quast

#!/usr/bin/python

import os
from common import run_quast, contigs_1k_2, assert_metric

name = os.path.basename(__file__)[5:-3]

run_quast(name, contigs=[contigs_1k_2], params='-R reference_1k.fa')
assert_metric(name, 'NGA50', ['760'])

run_quast(name, contigs=[contigs_1k_2], params='-R reference_1k.fa.gz')
assert_metric(name, 'NGA50', ['760'])

Beispiel #4

Datei: test_genes_another_id.py Projekt: ctb/quast

#!/usr/bin/python

import os
from common import run_quast, contigs_1k_2, reference_1k, assert_metric

name = os.path.basename(__file__)[5:-3]


run_quast(name, contigs=[contigs_1k_2], params='-R ' + reference_1k + ' -G genes_1k_verbose_id_does_not_match.gff')
assert_metric(name, '# genes', ['1 + 1 part'])

Beispiel #5

Datei: test_genes_txt.py Projekt: trocialba/quast

#!/usr/bin/python

import os
from common import run_quast, contigs_1k_2, reference_1k, assert_metric

name = os.path.basename(__file__)[5:-3]

run_quast(name,
          contigs=[contigs_1k_2],
          params='-R ' + reference_1k + ' -G genes_1k.txt')
assert_metric(name, '# genomic features', ['1 + 1 part'])