def test_embl_to_gb(self):
# EMBL records have more features than genbank, (ex more than one date,
# embl class, DOI cross references) so I can't convert an embl to gb
# and then to embl keeping all those data. But I can start from
# genbank record
# do embl file -> embl object -> gb file -> gb object ->
# embl file. Ensure that first and last files are identical
embl = DNA.read(self.single_rna_simple_fp, format="embl")
# "write" genbank record in a embl file
with io.StringIO() as fh:
DNA.write(embl, format="genbank", file=fh)
# read genbank file
fh.seek(0)
genbank = DNA.read(fh, format="genbank")
# "write" genbank record in a embl file
with io.StringIO() as fh:
DNA.write(genbank, format="embl", file=fh)
# read file object
obs = fh.getvalue()
# test objects
with open(self.single_rna_simple_fp) as fh:
exp = fh.read()
self.assertEqual(exp, obs)
def test_embl_to_gb(self):
# EMBL records have more features than genbank, (ex more than one date,
# embl class, DOI cross references) so I can't convert an embl to gb
# and then to embl keeping all those data. But I can start from
# genbank record
# do embl file -> embl object -> gb file -> gb object ->
# embl file. Ensure that first and last files are identical
embl = DNA.read(self.single_rna_simple_fp, format="embl")
# "write" genbank record in a embl file
with io.StringIO() as fh:
DNA.write(embl, format="genbank", file=fh)
# read genbank file
fh.seek(0)
genbank = DNA.read(fh, format="genbank")
# "write" genbank record in a embl file
with io.StringIO() as fh:
DNA.write(genbank, format="embl", file=fh)
# read file object
obs = fh.getvalue()
# test objects
with open(self.single_rna_simple_fp) as fh:
exp = fh.read()
self.assertEqual(exp, obs)
def reformat_egid(genbank_fp,
output_dir):
""" Reformat input genome to the formats accepted by EGID.
Parameters
----------
genbank_fp: string
file path to genome in GenBank format
output_dir: string
output directory path
Notes
-----
Input to EGID are five obsolete NCBI standard files: gbk, fna, faa, ffn
and ptt.
"""
(gb, genes) = _merge_genbank_seqs(genbank_fp)
DNA.write(gb, join(output_dir, 'id.fna'), format='fasta')
DNA.write(gb, join(output_dir, 'id.gbk'), format='genbank')
nucl_seq = str(gb)
output_f = {}
for x in ('faa', 'ffn', 'ptt'):
output_f[x] = open(join(output_dir, 'id.' + x), 'w')
output_f['ptt'].write('locus001\n' + str(len(genes)) + ' proteins\n')
# a ptt file contains the following columns:
fields = ('Location', 'Strand', 'Length', 'PID', 'Gene', 'Synonym',
'Code', 'COG', 'Product')
output_f['ptt'].write('\t'.join(fields) + '\n')
gid = 1 # assign an incremental integer to the current gene
for (gene, l) in sorted(genes.items(), key=lambda x: x[1][1]):
output_f['faa'].write('>' + gene + '\n' + l[0] + '\n')
output_f['ptt'].write(str(l[1]) + '..' + str(l[2]) + '\t' +
l[3] + '\t' + str(len(l[0])) + '\t' +
str(gid) + '\t-\tgene' + str(gid) +
'\t-\t-\t-\n')
if l[3] == '+': # positive strand
output_f['ffn'].write('>locus001:' + str(l[1]) + '-' +
str(l[2]) + '\n' +
nucl_seq[l[1]-1:l[2]] + '\n')
else: # negative strand (reverse complement)
rc_seq = str(DNA(nucl_seq[l[1]-1:l[2]]).reverse_complement())
output_f['ffn'].write('>locus001:c' + str(l[2]) + '-' +
str(l[1]) + '\n' + rc_seq + '\n')
gid += 1
for x in output_f:
output_f[x].close()
def reformat_genemark(genbank_fp, output_dir):
""" Reformat input genome to the formats accepted by GeneMark.
Parameters
----------
genbank_fp: string
file path to genome in GenBank format
output_dir: string
output directory path
Notes
-----
GeneMark's acceptable input file format is FASTA (genome sequence).
"""
gb = _merge_genbank_seqs(genbank_fp)[0]
DNA.write(gb, join(output_dir, 'id.fna'), format='fasta')
DNA.write(gb, join(output_dir, 'id.gbk'), format='genbank')
def reformat_genemark(genbank_fp,
output_dir):
""" Reformat input genome to the formats accepted by GeneMark.
Parameters
----------
genbank_fp: string
file path to genome in GenBank format
output_dir: string
output directory path
Notes
-----
GeneMark's acceptable input file format is FASTA (genome sequence).
"""
gb = _merge_genbank_seqs(genbank_fp)[0]
DNA.write(gb, join(output_dir, 'id.fna'), format='fasta')
DNA.write(gb, join(output_dir, 'id.gbk'), format='genbank')
def test_gb_to_embl(self):
genbank = DNA.read(self.genbank_fp, format="genbank")
with io.StringIO() as fh:
DNA.write(genbank, format="embl", file=fh)
# EMBL can't deal with genbank version (ie M14399.1 GI:145229)
# read embl data and write to gb
fh.seek(0)
embl = DNA.read(fh, format="embl")
with io.StringIO() as fh:
DNA.write(embl, format="genbank", file=fh)
# read gb data
obs = fh.getvalue()
with open(self.genbank_fp) as fh:
exp = fh.read()
self.assertEqual(exp, obs)
def test_gb_to_embl(self):
genbank = DNA.read(self.genbank_fp, format="genbank")
with io.StringIO() as fh:
DNA.write(genbank, format="embl", file=fh)
# EMBL can't deal with genbank version (ie M14399.1 GI:145229)
# read embl data and write to gb
fh.seek(0)
embl = DNA.read(fh, format="embl")
with io.StringIO() as fh:
DNA.write(embl, format="genbank", file=fh)
# read gb data
obs = fh.getvalue()
with open(self.genbank_fp) as fh:
exp = fh.read()
self.assertEqual(exp, obs)
