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import unittest
import shutil
import os
import subprocess
from Bio import SeqIO
# single, leftright
# fasta, fastq
# one file, two files
# forward, reverse
# clear, gzip, bzip
class TestTrinityPrepFlag(unittest.TestCase):
@classmethod
def setUpClass(cls):
try:
os.remove('coverage.log')
except:
pass
def tearDown(self):
shutil.rmtree('trinity_out_dir', True)
#pass
def test_fastq(self):
self.trinity("left1.fq", "fq")
self.assertEquals(30575, self.count_seqs(), "Unexpected sequence count")
def test_fastq_gz(self):
self.trinity("left1.fq.gz", "fq")
self.assertEquals(30575, self.count_seqs(), "Unexpected sequence count")
def test_fastq_bz2(self):
self.trinity("left1.fq.bz2", "fq")
self.assertEquals(30575, self.count_seqs(), "Unexpected sequence count")
def test_fastq_multiple_files_single(self):
self.trinity("left1.fq,left1.fq.gz", "fq")
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_fastq_multiple_files_single_bz2(self):
self.trinity("left1.fq.bz2,left1.fq.gz", "fq")
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_fastq_multiple_files_single_reverse(self):
self.trinity("left1.fq,left1.fq.gz", "fq", True)
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_fasta(self):
self.trinity("left1.fa")
self.assertEquals(30575, self.count_seqs(), "Unexpected sequence count")
def test_fasta_gz(self):
self.trinity("left1.fa.gz")
self.assertEquals(30575, self.count_seqs(), "Unexpected sequence count")
def test_fasta_multiple_files_single(self):
self.trinity("left1.fa,left1.fa.gz")
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_fasta_multiple_files_single_reverse(self):
self.trinity("left1.fa,left1.fa.gz", reverse=True)
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_paired_fastq(self):
self.trinity("left1.fq", "fq", morefiles="right1.fq")
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_paired_fastq_gz(self):
self.trinity("left1.fq.gz", "fq", morefiles="right1.fq.gz")
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_fastq_multiple_files_paired(self):
self.trinity("left1.fq,left1.fq.gz", "fq", morefiles="right1.fq,right1.fq.gz")
self.assertEquals(122300, self.count_seqs(), "Unexpected sequence count")
def test_fastq_multiple_files_paired_reverse(self):
self.trinity("left1.fq,left1.fq.gz", "fq", reverse=True, morefiles="right1.fq,right1.fq.gz")
self.assertEquals(122300, self.count_seqs(), "Unexpected sequence count")
def test_fasta_paired(self):
self.trinity("left1.fa", morefiles="right1.fa")
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_paired_sequences_have_1_or_2_extension(self):
self.trinity("sra_test.fq", morefiles="sra_test2.fq", seqtype='fq')
self.assertEquals(0, self.count_bad_endings(), "Found sequences with bad endings")
def test_fasta_gz_paired(self):
self.trinity("left1.fa.gz", morefiles="right1.fa.gz")
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_fasta_multiple_files_paired(self):
self.trinity("left1.fa,left1.fa.gz", morefiles="right1.fa,right1.fa.gz")
self.assertEquals(61150, self.count_seqs(), "Unexpected sequence count")
def test_fasta_multiple_files_paired(self):
self.trinity("left1.fa,left1.fa.gz", morefiles="right1.fa,right1.fa.gz", reverse=True)
self.assertEquals(122300, self.count_seqs(), "Unexpected sequence count")
def trinity(self, files, seqtype='fa', reverse=False, morefiles=None):
if morefiles:
tpl = "Trinity --left %s --right %s --prep --seqType %s --max_memory 2G --no_version_check --no_normalize_reads"
cmdline = tpl % (files, morefiles, seqtype)
else:
tpl = "Trinity --single %s --prep --seqType %s --max_memory 2G --no_version_check --no_normalize_reads"
cmdline = tpl % (files, seqtype)
if reverse:
cmdline += " --SS_lib_type " + ('RF' if morefiles else 'R')
print "Command line:", cmdline
with open("coverage.log", 'a') as file_out:
subprocess.call(cmdline,shell=True, stdout=file_out)
def count_seqs(self):
f = "trinity_out_dir/single.fa"
if os.path.isfile(f):
handle = open(f, "rU")
else:
handle = open("trinity_out_dir/both.fa", "rU")
seq_count = len([x for x in SeqIO.parse(handle, "fasta")])
handle.close()
return seq_count
def count_bad_endings(self):
f = "trinity_out_dir/single.fa"
if os.path.isfile(f):
handle = open(f, "rU")
else:
handle = open("trinity_out_dir/both.fa", "rU")
seq_count = len(list(x for x in SeqIO.parse(handle, "fasta") if not (x.id.endswith('/1') or x.id.endswith('/2'))))
handle.close()
return seq_count
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