Mercurial > repos > jpayne > gtsubsampler

comparison subsamplr.py @ 5:3852b3edc8a4 tip

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"planemo upload for repository https://toolrepo.galaxytrakr.org/"
author jpayne
date Fri, 19 Feb 2021 17:51:59 -0500
parents a90a883f88f9
children
comparison
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4:a90a883f88f9 5:3852b3edc8a4
41 fin, rin, fout, rout, cov, gen_size, *opts = argv[1:] 41 fin, rin, fout, rout, cov, gen_size, *opts = argv[1:]
42 ins = [fin, rin] 42 ins = [fin, rin]
43 outs = [fout, rout] 43 outs = [fout, rout]
44 except ValueError: # not enough values to unpack 44 except ValueError: # not enough values to unpack
45 try: 45 try:
46 fin, fout, cov, gen_size, *ops = argv[1:] 46 fin, fout, cov, gen_size, *opts = argv[1:]
47 ins = [fin] 47 ins = [fin]
48 outs = [fout] 48 outs = [fout]
49 except ValueError: 49 except ValueError:
50 print(usage) 50 print(usage)
51 quit(1) 51 quit(1)
68 ins = [stack.enter_context(openn(path, 'r')) for openn, path in zip(file_openers, ins)] # opened input files 68 ins = [stack.enter_context(openn(path, 'r')) for openn, path in zip(file_openers, ins)] # opened input files
69 inns = [iter(grouper(inn, 4)) for inn in ins] # stateful 4-ply iterator over lines in the input 69 inns = [iter(grouper(inn, 4)) for inn in ins] # stateful 4-ply iterator over lines in the input
70 outs = [stack.enter_context(openn(path, 'w')) for openn, path in zip(file_openers, outs)] # opened output files 70 outs = [stack.enter_context(openn(path, 'w')) for openn, path in zip(file_openers, outs)] # opened output files
71 71
72 for file in ins: 72 for file in ins:
73 print(file.name) 73 if hasattr(file, "name"):
74 print(file.name)
74 75
75 # https://en.m.wikipedia.org/wiki/Reservoir_sampling 76 # https://en.m.wikipedia.org/wiki/Reservoir_sampling
76 77
77 reservoir = [] 78 reservoir = []
78 # this is going to be 1 or 2-tuples of 4-tuples representing the 4 lines of the fastq file 79 # this is going to be 1 or 2-tuples of 4-tuples representing the 4 lines of the fastq file