Mercurial > repos > vimalkumarvelayudhan > riboplot

annotate tests/test_ribocount.py @ 17:6e3b13906b54

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Use packages from the test toolshed. Add bedtools dependency
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Fri, 28 Aug 2015 11:07:26 +0100
parents 628f82e72d72
children
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61c47a1d6a7a Add a test to check if a valid FASTA file is used (ribocount)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
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1 import os
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2 import logging
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3 import unittest
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5 from riboplot import ribocore, riboplot, ribocount
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7 # use testing configuration
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8 CONFIG = ribocount.CONFIG = riboplot.config.TestingConfig()
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9 logging.disable(logging.CRITICAL)
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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11 RIBO_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hRPFsorted.bam')
628f82e72d72 Version as released on PyPI 0.1.0
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12 RNA_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hmRNAsorted.bam')
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13 TRANSCRIPT_NAME = 'gi|148357119|ref|NM_001098396.1|'
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14 TRANSCRIPTOME_FASTA = os.path.join(CONFIG.TEST_DATA_DIR, 'zebrafish.fna')
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15 TRANSCRIPTOME_FASTA_MINUS1 = os.path.join(CONFIG.TEST_DATA_DIR, 'zebrafish_minus1.fna')
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16 UNRELATED_FASTA = os.path.join(CONFIG.TEST_DATA_DIR, 'unrelated.fna')
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61c47a1d6a7a Add a test to check if a valid FASTA file is used (ribocount)
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61c47a1d6a7a Add a test to check if a valid FASTA file is used (ribocount)
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19 class RiboCountTestCase(unittest.TestCase):
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21 def test_unrelated_fasta_file(self):
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22 """If an unrelated fasta file is used, raise an error"""
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23 parser = ribocount.create_parser()
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24 args = parser.parse_args(['-b', RIBO_FILE, '-f', UNRELATED_FASTA])
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25 self.assertRaises(ribocore.ArgumentError, ribocount.main, args)