def test_append_accession_and_version(self):
temp_gb2 = os.path.join(self.scan_ref_dir, "temp_acessioned.gb")
append_accession_and_version(accession="BA000007.2",
ingb=self.no_accession_gb,
finalgb=temp_gb2)
self.assertEqual(md5(temp_gb2), md5(self.with_accession_gb))
self.to_be_removed.append(temp_gb2)
def test_merge_outfiles(self):
"""
"""
merged_tab = merge_outfiles(
filelist=[self.test_combine, self.test_combine],
outfile=os.path.join(self.score_ref_dir, "temp_combined.tab"))
self.assertEqual(
md5(os.path.join(self.score_ref_dir, "test_combined.tab")),
md5(merged_tab))
self.to_be_removed.append(merged_tab)
def test_append_replacement_contigs(self):
outfile = os.path.join(self.test_dir, "contigs_minus_NODE_3.fasta")
remove_bad_contig(
infile=self.bad_fasta,
# outfile=self.good_fasta,
outfile=outfile,
# bad_name="NODE_3_length_222_cov_5.70526",
bad_name="NODE_3_",
logger=logger)
append_replacement_contigs(infile=self.good_fasta,
outfile=outfile,
name_list="NODE_4_:NODE_5_".split(":"),
logger=logger)
self.assertEqual(
md5(outfile),
md5(os.path.join(self.ref_dir, "ref_swapped_contigs.fasta")))
self.to_be_removed.append(outfile)
def test_combine_gbs(self):
temp_gb = os.path.join(self.scan_ref_dir, "temp_combined.gb")
combine_gbs(finalgb=temp_gb,
gb_list=[self.no_locus_gff, self.with_locus_gff])
self.assertEqual(md5(temp_gb), md5(self.combined_file))
def test_add_locus_tags_to_gff(self):
"""check with executable"""
add_locus_tags_to_gff(gff=self.no_locus_gff, acc="BA000007.2")
new_gff = str(os.path.splitext(self.no_locus_gff)[0] + "_tagged.gff")
self.assertEqual(md5(new_gff), md5(self.with_locus_gff))
self.to_be_removed.append(new_gff)