Mercurial > repos > vimalkumarvelayudhan > riboplot
annotate tests/test_riboplot.py @ 16:ef39290c19af
Replace docs with include directives (rst)
| author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
|---|---|
| date | Thu, 27 Aug 2015 13:03:28 +0100 |
| parents | 628f82e72d72 |
| children |
| rev | line source |
|---|---|
| 3 | 1 import os |
| 2 import shutil | |
| 3 import logging | |
| 4 import unittest | |
| 5 import tempfile | |
| 6 | |
| 7 from riboplot import ribocore, riboplot | |
| 8 | |
| 9 # use testing configuration | |
| 10 CONFIG = riboplot.CONFIG = riboplot.config.TestingConfig() | |
| 11 logging.disable(logging.CRITICAL) | |
| 12 | |
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13 RIBO_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hRPFsorted.bam') |
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14 RNA_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hmRNAsorted.bam') |
| 3 | 15 TRANSCRIPT_NAME = 'gi|148357119|ref|NM_001098396.1|' |
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16 TRANSCRIPTOME_FASTA = os.path.join(CONFIG.TEST_DATA_DIR, 'zebrafish.fna') |
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628f82e72d72
Version as released on PyPI 0.1.0
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17 UNRELATED_BAM = os.path.join(CONFIG.TEST_DATA_DIR, 'unrelated.bam') |
| 3 | 18 |
| 19 | |
| 20 class CheckArgumentsTestCase(unittest.TestCase): | |
| 21 """Check if all arguments sent on the command line are valid.""" | |
| 22 parser = riboplot.create_parser() | |
| 23 | |
| 24 def test_bedtools_missing(self): | |
| 25 """If bedtools is not in PATH, raise an error.""" | |
| 26 args = self.parser.parse_args( | |
| 27 ['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', RNA_FILE]) | |
| 28 save_path = os.environ['PATH'] | |
| 29 os.environ['PATH'] = '' | |
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Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
Vimalkumar Velayudhan <vimal@biotechcoder.com>
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30 self.assertRaises(OSError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file) |
| 3 | 31 os.environ['PATH'] = save_path |
| 32 | |
| 33 def test_is_bam_valid(self): | |
| 34 """Test if BAM file is valid.""" | |
| 35 valid = ribocore.is_bam_valid(RIBO_FILE) | |
| 36 self.assertTrue(valid) | |
| 37 | |
| 38 # test with a FASTA file (which is not BAM) | |
| 39 self.assertRaises(ValueError, ribocore.is_bam_valid, TRANSCRIPTOME_FASTA) | |
| 40 | |
| 41 def test_bam_has_index(self): | |
| 42 """Check if BAM file has an index.""" | |
| 43 # RPF file has an index | |
| 44 has_index = ribocore.bam_has_index(RIBO_FILE) | |
| 45 self.assertTrue(has_index) | |
| 46 | |
| 47 # RNA file doesn't have an index | |
| 48 has_index = ribocore.bam_has_index(RNA_FILE) | |
| 49 self.assertFalse(has_index) | |
| 50 | |
| 51 def test_create_bam_index(self): | |
| 52 """Index a BAM file.""" | |
| 53 ribocore.create_bam_index(RNA_FILE) | |
| 54 | |
| 55 # check if index exists | |
| 56 has_index = ribocore.bam_has_index(RNA_FILE) | |
| 57 self.assertTrue(has_index) | |
| 58 | |
| 59 # remove index | |
| 60 os.remove('{}.bai'.format(RNA_FILE)) | |
| 61 | |
| 62 def test_valid_read_length(self): | |
| 63 """Read length should be a valid integer.""" | |
| 64 args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, | |
| 65 '-t', TRANSCRIPT_NAME, '-l', '28']) | |
| 66 ribocore.check_optional_arguments(ribo_file=args.ribo_file, read_length=args.read_length) | |
| 67 | |
| 68 def test_invalid_read_length(self): | |
| 69 """An error is raised if an invalid read length is used.""" | |
| 70 args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, | |
| 71 '-l', '-1']) # invalid read length -1 | |
| 72 self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, | |
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096c6bbf4a04
Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
6
diff
changeset
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73 ribo_file=args.ribo_file, read_length=args.read_length) |
| 3 | 74 |
| 75 args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, | |
| 76 '-l', '100']) # invalid read length 100 | |
| 77 self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, | |
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096c6bbf4a04
Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
6
diff
changeset
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78 ribo_file=args.ribo_file, read_length=args.read_length) |
| 3 | 79 |
| 80 def test_valid_read_offset(self): | |
| 81 """Read offset should be positive.""" | |
| 82 args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, | |
| 83 '-s', '-1']) # invalid read offset -1 | |
| 84 self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, | |
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096c6bbf4a04
Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
6
diff
changeset
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85 ribo_file=args.ribo_file, read_offset=args.read_offset) |
| 3 | 86 |
| 87 def test_is_fasta_valid(self): | |
| 88 """A valid FASTA file can be opened with pysam.FastaFile.""" | |
| 89 self.assertTrue(ribocore.is_fasta_valid(TRANSCRIPTOME_FASTA)) | |
| 90 | |
| 91 def test_missing_transcript_in_fasta(self): | |
| 92 """If a transcript is missing in FASTA, an error is raised.""" | |
| 93 args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME]) # invalid read offset -1 | |
| 94 self.assertRaises(ribocore.ArgumentError, ribocore.check_required_arguments, | |
| 95 args.ribo_file, args.transcriptome_fasta, 'hello') | |
| 96 | |
| 97 def test_missing_transcript_in_bam(self): | |
| 98 """If a transcript is missing in BAM, an error is raised.""" | |
| 99 # testing with an unrelated BAM file | |
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Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
12
diff
changeset
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100 args = self.parser.parse_args(['-b', UNRELATED_BAM, '-f', TRANSCRIPTOME_FASTA, |
| 3 | 101 '-t', TRANSCRIPT_NAME]) |
| 102 self.assertRaises(ribocore.ArgumentError, ribocore.check_required_arguments, args.ribo_file, | |
| 103 args.transcriptome_fasta, args.transcript_name) | |
| 104 | |
| 105 | |
| 106 class RNACountsTestCase(unittest.TestCase): | |
| 107 | |
| 108 def test_get_rna_counts(self): | |
| 109 """Test get RNA counts for transcript from RNA-Seq BAM file. Assumes bedtools is installed.""" | |
| 110 counts = riboplot.get_rna_counts(RNA_FILE, TRANSCRIPT_NAME) | |
| 111 self.assertIsInstance(counts, dict) | |
| 112 self.assertTrue(len(counts) > 0) | |
| 113 | |
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2ffa8172dce1
Tests for valid RNA Seq bam and warnings when there are no RNA counts
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
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diff
changeset
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114 def test_invalid_rna_file(self): |
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2ffa8172dce1
Tests for valid RNA Seq bam and warnings when there are no RNA counts
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
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diff
changeset
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115 """If an invalid RNA file is provided, generate an error message""" |
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2ffa8172dce1
Tests for valid RNA Seq bam and warnings when there are no RNA counts
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
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diff
changeset
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116 # using transcriptome FASTA file as the invalid RNA file for test |
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2ffa8172dce1
Tests for valid RNA Seq bam and warnings when there are no RNA counts
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
3
diff
changeset
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117 parser = riboplot.create_parser() |
|
2ffa8172dce1
Tests for valid RNA Seq bam and warnings when there are no RNA counts
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
3
diff
changeset
|
118 args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', TRANSCRIPTOME_FASTA]) |
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7
096c6bbf4a04
Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
6
diff
changeset
|
119 self.assertRaises(ValueError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file) |
| 3 | 120 |
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Add a test to check if a valid FASTA file is used (ribocount)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
7
diff
changeset
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121 |
| 3 | 122 class RiboPlotTestCase(unittest.TestCase): |
| 123 | |
| 124 def test_get_codon_positions(self): | |
| 125 """Get codon positions in all frames given a sequence.""" | |
| 126 # the positions on this sequence were calculated manually. | |
| 127 fasta = ('AACCGGAGCACCCAGAGAAAACCCACGCAAACGCAGGGAGAATTTGCAAACTCCACACA' | |
| 128 'GAAATGCCAGCTGATCCAGCCGAGCCTCGAGTCAGCATCCTTGCTTGTTGGATGCCTGA' | |
| 129 'TTGCAGTTCAACTCCAAACTCAGTTGGACCAGCTGATCAGTG') | |
| 130 codon_positions = riboplot.get_start_stops(fasta) | |
| 131 expected = {1: {'starts': [], 'stops': []}, | |
| 132 2: {'starts': [], 'stops': [71, 116, 152]}, | |
| 133 3: {'starts': [63, 111], 'stops': []}} | |
| 134 self.assertEqual(codon_positions, expected) | |
| 135 | |
| 136 def test_valid_riboplot_run(self): | |
| 137 """A good riboplot run""" | |
| 138 output_dir = tempfile.mkdtemp() | |
| 139 print 'Output path is {}'.format(output_dir) | |
| 140 parser = riboplot.create_parser() | |
| 141 args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, | |
| 142 '-o', output_dir]) | |
| 143 riboplot.main(args) | |
| 144 for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'): | |
| 145 self.assertTrue(os.path.exists(os.path.join(output_dir, fname))) | |
| 146 shutil.rmtree(output_dir) | |
| 147 | |
| 148 def test_transcript_with_no_counts(self): | |
| 149 """If the transcript has no ribocounts, no plot should be produced.""" | |
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Add a test to check if a valid FASTA file is used (ribocount)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
7
diff
changeset
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150 transcript = 'gi|62955616|ref|NM_001017822.1|' # has no reads |
| 3 | 151 output_dir = tempfile.mkdtemp() |
| 152 parser = riboplot.create_parser() | |
| 153 args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', transcript, '-o', output_dir]) | |
| 154 self.assertRaises(ribocore.RiboPlotError, riboplot.main, args) | |
| 155 for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'): | |
| 156 self.assertFalse(os.path.exists(os.path.join(output_dir, fname))) | |
| 157 shutil.rmtree(output_dir) |