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)