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test_autoskewer.py
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import os
from subprocess import call
from os.path import exists
def test_cmdline1Q():
call("autoskewer.py -i example/sample.fastq".split())
assert os.path.exists("example/sample.scrubbed.fastq")
assert os.path.exists("example/sample.scrubbed.log")
os.remove("example/sample.scrubbed.fastq")
os.remove("example/sample.scrubbed.log")
def test_cmdline1A():
call("autoskewer.py -i example/sample.fasta".split())
assert os.path.exists("example/sample.scrubbed.fasta")
assert os.path.exists("example/sample.scrubbed.log")
os.remove("example/sample.scrubbed.fasta")
os.remove("example/sample.scrubbed.log")
def test_cmdline2A():
call("autoskewer.py -i example/sample.fa".split())
assert os.path.exists("example/sample.fa.scrubbed.fasta")
assert os.path.exists("example/sample.fa.scrubbed.log")
os.remove("example/sample.fa.scrubbed.fasta")
os.remove("example/sample.fa.scrubbed.log")
def test_cmdline2Q():
call("autoskewer.py -i example/sample.fq".split())
assert os.path.exists("example/sample.fq.scrubbed.fastq")
assert os.path.exists("example/sample.fq.scrubbed.log")
os.remove("example/sample.fq.scrubbed.fastq")
os.remove("example/sample.fq.scrubbed.log")
def test_cmdline3Q():
call("autoskewer.py example/sample.fastq".split())
assert os.path.exists("example/sample.scrubbed.fastq")
assert os.path.exists("example/sample.scrubbed.log")
os.remove("example/sample.scrubbed.fastq")
os.remove("example/sample.scrubbed.log")
def test_cmdline3A():
call("autoskewer.py example/sample.fasta".split())
assert os.path.exists("example/sample.scrubbed.fasta")
assert os.path.exists("example/sample.scrubbed.log")
os.remove("example/sample.scrubbed.fasta")
os.remove("example/sample.scrubbed.log")
def test_cmdline4A():
call("autoskewer.py example/sample.fa".split())
assert os.path.exists("example/sample.fa.scrubbed.fasta")
assert os.path.exists("example/sample.fa.scrubbed.log")
os.remove("example/sample.fa.scrubbed.fasta")
os.remove("example/sample.fa.scrubbed.log")
def test_cmdline4Q():
call("autoskewer.py example/sample.fq".split())
assert os.path.exists("example/sample.fq.scrubbed.fastq")
assert os.path.exists("example/sample.fq.scrubbed.log")
os.remove("example/sample.fq.scrubbed.fastq")
os.remove("example/sample.fq.scrubbed.log")
def test_cmdline_explicit1Q():
call("autoskewer.py -i example/sample.fastq -o example/sample-processed.fastq".split())
assert os.path.exists("example/sample-processed.fastq")
assert os.path.exists("example/sample-processed.log")
os.remove("example/sample-processed.fastq")
os.remove("example/sample-processed.log")
def test_cmdline_explicit1A():
call("autoskewer.py -i example/sample.fasta -o example/sample-processed.fasta".split())
assert os.path.exists("example/sample-processed.log")
os.remove("example/sample-processed.fasta")
os.remove("example/sample-processed.log")
def test_cmdline_explicit2A():
call("autoskewer.py -i example/sample.fa -o example/sample-processed.fasta".split())
assert os.path.exists("example/sample-processed.log")
os.remove("example/sample-processed.fasta")
os.remove("example/sample-processed.log")
def test_cmdline_explicit2Q():
call("autoskewer.py -i example/sample.fq -o example/sample-processed.fastq".split())
assert os.path.exists("example/sample-processed.log")
os.remove("example/sample-processed.fastq")
os.remove("example/sample-processed.log")