Exemplo n.º 1
0
 def test_outputbasename(self):
     ''' Test that the outputfile parameter works with just a basename '''
     os.mkdir('basename')
     os.symlink(self.sff, os.path.join('basename', 'sff1.sff'))
     outfile = bwa.compile_reads('basename', 'outputfile.fastq')
     eq_('outputfile.fastq', outfile)
     eq_(seqio.reads_in_file(self.sff), seqio.reads_in_file(outfile))
Exemplo n.º 2
0
 def test_outputabsrelpath(self):
     ''' Test that the outputfile parameter works with a relative or abs path '''
     os.mkdir('absrel')
     os.symlink(self.sff, os.path.join('absrel', 'sff1.sff'))
     outfile = bwa.compile_reads('absrel', 'absrel/outputfile.fastq')
     eq_('absrel/outputfile.fastq', outfile)
     eq_(seqio.reads_in_file(self.sff),
         seqio.reads_in_file('absrel/outputfile.fastq'))
Exemplo n.º 3
0
    def test_paramdirfastqonly(self):
        ''' Directory of only fastq '''
        os.mkdir('fastq')
        os.symlink(self.fastq, os.path.join('fastq', 'fq1.fastq'))
        os.symlink(self.fastq, os.path.join('fastq', 'fq2.fastq'))
        outfile = bwa.compile_reads('fastq')
        expected_readcount = seqio.reads_in_file(self.sff) * 2

        self._isfastq(outfile)
        eq_(expected_readcount, seqio.reads_in_file(outfile))
Exemplo n.º 4
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    def test_paramdirsffonly(self):
        ''' Directory of only sff files '''
        os.mkdir('sffs')
        os.symlink(self.sff, os.path.join('sffs', 'sff1.sff'))
        os.symlink(self.sff, os.path.join('sffs', 'sff2.sff'))
        outfile = bwa.compile_reads('sffs')
        expected_readcount = seqio.reads_in_file(self.sff) * 2

        self._isfastq(outfile)
        eq_(expected_readcount, seqio.reads_in_file(outfile))
Exemplo n.º 5
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    def test_paramdirmixed(self):
        ''' Directory of sff & fastq '''
        os.mkdir('mixed')
        os.symlink(self.sff, os.path.join('mixed', 'sff1.sff'))
        os.symlink(self.fastq, os.path.join('mixed', 'fq1.fastq'))
        outfile = bwa.compile_reads('mixed')
        expected_readcount = seqio.reads_in_file( self.sff ) + \
            seqio.reads_in_file( self.fastq )

        self._isfastq(outfile)
        eq_(expected_readcount, seqio.reads_in_file(outfile))
Exemplo n.º 6
0
 def readsinfiletest( self, fafile, expectedlines ):
     eq_( seqio.reads_in_file( fafile ), expectedlines )
Exemplo n.º 7
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 def readsinfiletest(self, fafile, expectedlines):
     eq_(seqio.reads_in_file(fafile), expectedlines)