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 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)
from __future__ import division
import os
import skbio
from skbio import DNA
mydir = os.path.expanduser("~/GitHub/LTDE/")
fa_path = mydir + 'data/align/reseq_sanger.fasta'
fa = skbio.io.read(fa_path, format='fasta')
KBS0710_8F = DNA.read(fa_path, seq_num=1)
KBS0710_1492R = DNA.read(fa_path, seq_num=2).complement(reverse=True)
KBS0721_8F = DNA.read(fa_path, seq_num=3)
KBS0721_1492R = DNA.read(fa_path, seq_num=4).complement(reverse=True)
print(KBS0721_8F)
print(KBS0721_1492R)
#print(len(KBS0721_8F))
#print(len(KBS0721_1492R))
from skbio import DNA
from skbio.alignment import global_pairwise_align_nucleotide
s1 = DNA.read("data/seq1")
s2 = DNA.read("data/seq2")
query = DNA("TTTTCTTGTTGATTCTGGTCCAGAGTAATCGCTTGAGTGTTG")
def pairwise_similarity(seq, query):
alignment = global_pairwise_align_nucleotide(seq, query)
return alignment[0].fraction_same(alignment[1])
print "seq1: %s\nseq2: %s" % (s1, s2)
print "seq1-query: %s" % pairwise_similarity(s1, query)
print "seq2-query: %s" % pairwise_similarity(s2, query)
