def test_composition(self):
from pbs import ls, wc
c1 = int(wc(ls("-A1"), l=True))
c2 = len(os.listdir("."))
if c1 != c2:
with open("/tmp/fail", "a") as h: h.write("F**K\n")
self.assertEqual(c1, c2)
def test_composition(self):
from pbs import ls, wc
c1 = int(wc(ls("-A1"), l=True))
c2 = len(os.listdir("."))
if c1 != c2:
with open("/tmp/fail", "a") as h:
h.write("F**K\n")
self.assertEqual(c1, c2)
def test_command_wrapper(self):
from pbs import Command, which
ls = Command(which("ls"))
wc = Command(which("wc"))
c1 = int(wc(ls(A=True), l=True))
c2 = len(os.listdir("."))
self.assertEqual(c1, c2)
def test_command_wrapper(self):
from pbs import Command, which
ls = Command(which("ls"))
wc = Command(which("wc"))
c1 = int(wc(ls("-A1"), l=True))
c2 = len(os.listdir("."))
self.assertEqual(c1, c2)
from Bio import SeqIO
import numpy as np
import scipy as sp
import scipy.stats
import matplotlib as mpl
mpl.use('agg')
import matplotlib.pyplot as plt
from pbs import wc
input_file = sys.argv[1]
output_file = sys.argv[2]
num_lines = int(wc(input_file, '-l').split()[0])
assert(num_lines % 4 == 0)
num_reads = num_lines / 4
if num_reads > 10000000:
idxs = set(sorted(random.sample(xrange(num_reads),10000000)))
qualities = []
for (i,record) in enumerate(SeqIO.parse(input_file, 'fastq')):
if num_reads <= 10000000 or i in idxs:
qualities.append(record.letter_annotations['phred_quality'])
if i % 10000 == 0:
sys.stdout.write("%i " % i)
sys.stdout.flush()
#!/usr/bin/env python
from pbs import ls, wc
def p(val, *fns):
for fn in fns:
val = fn(val)
return val
print p(ls(), wc())
def test_composition(self):
from pbs import ls, wc
c1 = int(wc(ls(A=True), l=True))
c2 = len(os.listdir("."))
self.assertEqual(c1, c2)
#!/usr/bin/env python
from pbs import ls, wc
def p(val, *fns):
for fn in fns:
val = fn(val)
return val
print p(ls(), wc())
