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from unittest import TestCase
from collections import namedtuple
import os
import shutil
import inspect
from seqcluster.prepare_data import _read_fastq_files, _create_matrix_uniq_seq
import seqcluster
class TestPreparedata(TestCase):
def test_preparedata(self):
out_dir = "test/test_out_prepare"
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
os.mkdir(out_dir)
arg = namedtuple('args', 'minl maxl minc out')
args = arg(15, 40, 1, out_dir)
seq_l, list_s = _read_fastq_files(open("data/examples/collapse/config"), args)
ma_out = open(os.path.join(out_dir, "seqs.ma"), 'w')
seq_out = open(os.path.join(out_dir, "seqs.fa"), 'w')
_create_matrix_uniq_seq(list_s, seq_l, ma_out, seq_out, 1)
self.assertTrue(os.path.exists(os.path.join(out_dir, "seqs.ma")))
self.assertTrue(os.path.exists(os.path.join(out_dir, "seqs.fa")))
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
test_preparedata.collapse = True
def test_umis(self):
from seqcluster.libs.fastq import collapse, write_output
umis = collapse(os.path.abspath("data/examples/umis/sample.fastq"))
if len(umis.keys()) != 2:
raise ValueError("umis didn't detect two unique sequences")
out_dir = "test/test_automated_output"
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
os.mkdir(out_dir)
write_output(os.path.join(out_dir, "umis.fastq"), umis)
test_umis.umis = True
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