1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
from Bio import SeqIO
import unittest
import os
class TestTrinitySampleData(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.sampledata_dir = os.environ["TRINITY_SAMPLEDATA"]
def test_genome_guided(self):
seq_count = self.count_sequences('test_GenomeGuidedTrinity', 'test_GG_use_bam_trinity_outdir',
'Trinity-GG.fasta')
self.assertTrue(50 <= seq_count <= 60, msg='Found %s sequences' % seq_count)
def test_genome_guided_with_jaccard_clipping(self):
seq_count = self.count_sequences('test_GenomeGuidedTrinity', 'test_Schizo_trinityGG_jaccard_RF_outdir',
'Trinity-GG.fasta')
self.assertTrue(60 <= seq_count <= 80, msg='Found %s sequences' % seq_count)
def test_paired_end_normalization(self):
seq_count = self.count_sequences('test_InSilicoReadNormalization',
'reads.left.fq.gz.normalized_K25_C5_pctSD200.fq')
self.assertTrue(35 <= seq_count <= 50, msg='Found %s sequences' % seq_count)
seq_count = self.count_sequences('test_InSilicoReadNormalization',
'reads.right.fq.gz.normalized_K25_C5_pctSD200.fq')
self.assertTrue(30 <= seq_count <= 40, msg='Found %s sequences' % seq_count)
seq_count = self.count_sequences('test_InSilicoReadNormalization',
'reads.single.fq.normalized_K25_C5_pctSD200.fq')
self.assertTrue(50 <= seq_count <= 65, msg='Found %s sequences' % seq_count)
def test_trinity_assembly(self):
seq_count = self.count_sequences('test_Trinity_Assembly', 'trinity_out_dir', 'Trinity.fasta')
self.assertTrue(100 <= seq_count <= 120, msg='Found %s sequences' % seq_count)
def test_DE_analysis_EdgeR(self):
check_file = os.path.join(self.sampledata_dir, 'test_DE_analysis', 'edgeR_outdir', 'numDE_feature_counts.P0.001_C2.matrix')
self.assertTrue(os.path.isfile(check_file), 'DE output file not created')
def test_align_and_estimate_abundance(self):
cats = ['PAIRED', 'SINGLE']
for cat in cats:
check_file = os.path.join(self.sampledata_dir, 'test_align_and_estimate_abundance',\
'%s_END_ABUNDANCE_ESTIMATION' % cat, 'RSEM-gene.counts.matrix')
self.assertTrue(os.path.isfile(check_file), 'RSEM-gene.counts.matrix not created')
def test_full_edgeR_pipeline(self):
check_file = os.path.join(self.sampledata_dir, 'test_full_edgeR_pipeline', 'read_content_analysis', 'read_content_analysis.nameSorted.bam')
self.assertTrue(os.path.isfile(check_file), 'edgeR sorted BAM not created')
### Helper methods
def count_sequences(self, *paths):
gg = os.path.join(self.sampledata_dir, *paths)
handle = open(gg, "rU")
seq_count = len([x for x in SeqIO.parse(handle, "fasta")])
handle.close()
return seq_count
|
