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#!/usr/bin/env python
import subprocess
def run_trinity_seqtk(inputfile, readdir):
cmd = "../seqtk-trinity seq -A -R {} {} > /dev/null".format(readdir, inputfile)
return subprocess.run(cmd, shell=True, check=False).returncode
## old format: @61DFRAAXX100204:1:100:10494:3070/1
def test_oldformat_1_success():
ret = run_trinity_seqtk("oldformat_1.fq", 1)
assert(ret==0)
def test_oldformat_1_failure():
ret = run_trinity_seqtk("oldformat_1.fq", 2)
assert(ret==2)
def test_oldformat_2_success():
ret = run_trinity_seqtk("oldformat_2.fq", 2)
assert(ret==0)
def test_oldformat_2_failure():
ret = run_trinity_seqtk("oldformat_2.fq", 1)
assert(ret==2)
## new format: @M01581:927:000000000-ARTAL:1:1101:19874:2078 1:N:0:1
def test_newformat_1_success():
ret = run_trinity_seqtk("newformat_1.fq", 1)
assert(ret==0)
def test_newformat_1_failure():
ret = run_trinity_seqtk("newformat_1.fq", 2)
assert(ret==2)
def test_newformat_2_success():
ret = run_trinity_seqtk("newformat_2.fq", 2)
assert(ret==0)
def test_newformat_2_failure():
ret = run_trinity_seqtk("newformat_2.fq", 1)
assert(ret==2)
## corrupt format tests
def test_corrupt_fastq():
ret = run_trinity_seqtk("corrupt_1.fq", 1)
assert(ret==4)
def test_unequal_seq_n_quals_fastq():
ret = run_trinity_seqtk("unequal_seq_n_quals_1.fq", 1)
assert(ret==3)
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