def test_iter_stream(self):
progress = MockProgress()
xphyle.configure(progress=True, progress_wrapper=progress)
with intercept_stdin('foo\nbar\nbaz'):
with xopen(STDIN, 'rt', context_wrapper=True,
compression=False) as o:
lines = list(o)
self.assertListEqual(['foo\n', 'bar\n', 'baz\n'], lines)
assert 3 == progress.count
def test_progress(self):
progress = MockProgress()
xphyle.configure(progress=True, progress_wrapper=progress)
path = self.root.make_file()
with open(path, 'wt') as o:
for i in range(100):
o.write(random_text())
compress_file(path, compression='gz', use_system=False)
assert 100 == progress.count
def test_progress_delmited(self):
progress = MockProgress()
xphyle.configure(progress=True, progress_wrapper=progress)
path = self.root.make_file()
with open(path, 'wt') as o:
for i in range(100):
o.write('row\t{}\n'.format(i))
rows = list(read_delimited(path))
assert 100 == len(rows)
assert 100 == progress.count
#!/usr/local/bin/python
import os, warnings, argparse, gzip, tqdm, xphyle
from Bio import SeqIO
from sys import argv
from Bio.Seq import Seq
from mimetypes import guess_type
from functools import partial
from xphyle import xopen
xphyle.configure(progress=True)
xphyle.configure(threads=4)
def rreplace(s, old, new, occurrence):
li = s.rsplit(old, occurrence)
return new.join(li)
def translate(fasta):
dbf = os.path.basename(rreplace(fasta, 'fasta', 'fasta.db', 1))
print('Translating...')
with xopen(dbf, 'wt') as db:
parser = SeqIO.parse(xopen(fasta, 'rt'), 'fasta')
for sequence in parser:
id, seq = sequence.description, Seq(
str(sequence.seq).upper().replace('X', 'N'))
f = (-3, -2, -1, 1, 2, 3)
for i in f:
if i < 0:
db.write('>%s\n%s\n' %
def setUp(self):
self.root = TempDir()
xphyle.configure(progress=False)