Ejemplo n.º 1
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    def test_indexing_to_custom_location_works(self):
        '''test indexing a file with a non-default location.'''

        index_path = get_temp_filename(suffix='custom.tbi')
        pysam.tabix_index(self.tmpfilename, preset="gff",
                          index=index_path, force=True)
        self.assertTrue(checkBinaryEqual(index_path, self.filename_idx))
        os.unlink(index_path)
Ejemplo n.º 2
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 def testSaveStdout(self):
     outfile = get_temp_filename(suffix=".tsv")
     r = pysam.samtools.flagstat(os.path.join(BAM_DATADIR, "ex1.bam"),
                                 save_stdout=outfile)
     self.assertEqual(r, None)
     with open(outfile) as inf:
         r = inf.read()
     self.assertTrue(len(r) > 0)
Ejemplo n.º 3
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 def testSaveStdout(self):
     outfile = get_temp_filename(suffix=".tsv")
     r = pysam.samtools.flagstat(
         os.path.join(DATADIR, "ex1.bam"),
         save_stdout=outfile)
     self.assertEqual(r, None)
     with open(outfile) as inf:
         r = inf.read()
     self.assertTrue(len(r) > 0)
Ejemplo n.º 4
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    def test_indexing_to_custom_location_works(self):
        '''test indexing a file with a non-default location.'''

        index_path = get_temp_filename(suffix='custom.tbi')
        pysam.tabix_index(self.tmpfilename,
                          preset="gff",
                          index=index_path,
                          force=True)
        self.assertTrue(checkGZBinaryEqual(index_path, self.filename_idx))
        os.unlink(index_path)
Ejemplo n.º 5
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    def test_read_can_be_written_to_file(self):
        tmpfilename = get_temp_filename(".bam")
        with pysam.AlignmentFile(tmpfilename, "wb",
                                 reference_names=["chr1", "chr2", "chr3"],
                                 reference_lengths=[1000, 2000, 3000]) as outf:
            read = self.build_read()
            read.reference_id = 2
            outf.write(read)

        stdout = pysam.samtools.view(tmpfilename)
        chromosome = stdout.split("\t")[2]
        self.assertEqual(chromosome, "chr3")
        os.unlink(tmpfilename)
Ejemplo n.º 6
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    def testConstructionFromCopy(self):

        fn_in = os.path.join(DATADIR, self.filename)
        fn_out = get_temp_filename(suffix=".vcf")
        vcf_in = pysam.VariantFile(fn_in)

        vcf_out = pysam.VariantFile(fn_out, "w", header=vcf_in.header)
        for record in vcf_in:
            vcf_out.write(record)

        vcf_out.close()

        self.complete_check(fn_in, fn_out)
Ejemplo n.º 7
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    def testConstructionFromCopy(self):

        fn_in = os.path.join(DATADIR, self.filename)
        fn_out = get_temp_filename(suffix=".vcf")
        vcf_in = pysam.VariantFile(fn_in)

        vcf_out = pysam.VariantFile(fn_out, "w", header=vcf_in.header)
        for record in vcf_in:
            vcf_out.write(record)

        vcf_out.close()

        self.complete_check(fn_in, fn_out)
Ejemplo n.º 8
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    def test_read_can_be_written_to_file(self):
        tmpfilename = get_temp_filename(".bam")
        with pysam.AlignmentFile(tmpfilename, "wb",
                                 reference_names=["chr1", "chr2", "chr3"],
                                 reference_lengths=[1000, 2000, 3000]) as outf:
            read = self.build_read()
            read.reference_id = 2
            outf.write(read)

        stdout = pysam.samtools.view(tmpfilename)
        chromosome = stdout.split("\t")[2]
        self.assertEqual(chromosome, "chr3")
        os.unlink(tmpfilename)
Ejemplo n.º 9
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    def test_open_file_with_explicit_abritrarily_named_index_succeeds(self):
        tmpfilename = get_temp_filename(self.data_suffix)
        shutil.copyfile(self.filename, tmpfilename)

        filepath_index = self.filename + ".fai"
        filepath_index_compressed = self.filename + ".gzi"
        if not os.path.exists(filepath_index_compressed):
            filepath_index_compressed = None
        with pysam.FastaFile(tmpfilename,
                             filepath_index=filepath_index,
                             filepath_index_compressed=filepath_index_compressed) as inf:
            self.assertEqual(len(inf), 2)

        # index should not be auto-generated
        self.assertFalse(os.path.exists(tmpfilename + ".fai"))
        os.unlink(tmpfilename)
Ejemplo n.º 10
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    def test_open_file_with_explicit_abritrarily_named_index_succeeds(self):
        tmpfilename = get_temp_filename(self.data_suffix)
        shutil.copyfile(self.filename, tmpfilename)

        filepath_index = self.filename + ".fai"
        filepath_index_compressed = self.filename + ".gzi"
        if not os.path.exists(filepath_index_compressed):
            filepath_index_compressed = None
        with pysam.FastaFile(tmpfilename,
                             filepath_index=filepath_index,
                             filepath_index_compressed=filepath_index_compressed) as inf:
            self.assertEqual(len(inf), 2)

        # index should not be auto-generated
        self.assertFalse(os.path.exists(tmpfilename + ".fai"))
        os.unlink(tmpfilename)
Ejemplo n.º 11
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    def check_read_write(self, flag_write, header):

        fn = get_temp_filename()
        with pysam.AlignmentFile(
                fn,
                flag_write,
                header=header,
                reference_filename=os.path.join(BAM_DATADIR, "ex1.fa")) as outf:
            a = pysam.AlignedSegment()
            a.query_name = "abc"
            outf.write(a)

        with pysam.AlignmentFile(fn) as inf:
            read_header = inf.header

        os.unlink(fn)
        self.compare_headers(header, read_header)
Ejemplo n.º 12
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    def check_read_write(self, flag_write, header):

        fn = get_temp_filename()
        with pysam.AlignmentFile(
                fn,
                flag_write,
                header=header,
                reference_filename=os.path.join(BAM_DATADIR, "ex1.fa")) as outf:
            a = pysam.AlignedSegment()
            a.query_name = "abc"
            outf.write(a)

        with pysam.AlignmentFile(fn) as inf:
            read_header = inf.header

        os.unlink(fn)
        self.compare_headers(header, read_header)
Ejemplo n.º 13
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    def testSingleThreadEqualsMultithreadResult(self):
        with pysam.VariantFile(self.filename) as inf:
            header = inf.header
            single = [r for r in inf]
        with pysam.VariantFile(self.filename, threads=2) as inf:
            multi = [r for r in inf]
        for r1, r2 in zip(single, multi):
            assert str(r1) == str(r2)

        bcf_out = get_temp_filename(suffix=".bcf")
        with pysam.VariantFile(bcf_out, mode='wb', header=header,
                               threads=2) as out:
            for r in single:
                out.write(r)
        with pysam.VariantFile(bcf_out) as inf:
            multi_out = [r for r in inf]
        for r1, r2 in zip(single, multi_out):
            assert str(r1) == str(r2)
Ejemplo n.º 14
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    def testConstructionWithRecords(self):

        fn_in = os.path.join(DATADIR, self.filename)
        fn_out = get_temp_filename(suffix=".vcf")
        vcf_in = pysam.VariantFile(fn_in)

        header = pysam.VariantHeader()

        for record in vcf_in.header.records:
            header.add_record(record)

        fn = str("tmp_VariantFileTest_testConstructionWithRecords") + ".vcf"
        vcf_out = pysam.VariantFile(fn, "w", header=header)
        for record in vcf_in:
            # currently segfaults here:
            # vcf_out.write(record)
            pass
        return

        vcf_out.close()
        self.complete_check(fn_in, fn_out)
Ejemplo n.º 15
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    def testConstructionWithRecords(self):

        fn_in = os.path.join(DATADIR, self.filename)
        fn_out = get_temp_filename(suffix=".vcf")
        vcf_in = pysam.VariantFile(fn_in)

        header = pysam.VariantHeader()

        for record in vcf_in.header.records:
            header.add_record(record)

        fn = str("tmp_VariantFileTest_testConstructionWithRecords") + ".vcf"
        vcf_out = pysam.VariantFile(fn, "w", header=header)
        for record in vcf_in:
            # currently segfaults here:
            # vcf_out.write(record)
            pass
        return

        vcf_out.close()
        self.complete_check(fn_in, fn_out)
Ejemplo n.º 16
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    def testConstructionWithLines(self):

        fn_in = os.path.join(CBCF_DATADIR, self.filename)
        fn_out = get_temp_filename(suffix=".vcf")
        vcf_in = pysam.VariantFile(fn_in)

        header = pysam.VariantHeader()
        for sample in vcf_in.header.samples:
            header.add_sample(sample)

        for hr in vcf_in.header.records:
            header.add_line(str(hr))

        vcf_out = pysam.VariantFile(fn_out, "w", header=header)

        for record in vcf_in:
            vcf_out.write(record)

        vcf_out.close()
        vcf_in.close()

        self.complete_check(fn_in, fn_out)
    def check_read_write(self, flag_write, header):

        fn = get_temp_filename()
        print(fn)
        with pysam.AlignmentFile(fn,
                                 flag_write,
                                 header=header,
                                 reference_filename=os.path.join(
                                     BAM_DATADIR, "ex1.fa")) as outf:
            a = pysam.AlignedSegment()
            a.query_name = "abc"
            outf.write(a)

        with pysam.AlignmentFile(fn) as inf:
            read_header = inf.header

        # os.unlink(fn)
        self.compare_headers(header, read_header)
        expected_lengths = dict([(x["SN"], x["LN"]) for x in header["SQ"]])
        self.assertEqual(
            expected_lengths,
            dict(zip(read_header.references, read_header.lengths)))
Ejemplo n.º 18
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    def testConstructionWithLines(self):

        fn_in = os.path.join(DATADIR, self.filename)
        fn_out = get_temp_filename(suffix=".vcf")
        vcf_in = pysam.VariantFile(fn_in)

        header = pysam.VariantHeader()
        for sample in vcf_in.header.samples:
            header.add_sample(sample)

        for hr in vcf_in.header.records:
            header.add_line(str(hr))

        vcf_out = pysam.VariantFile(fn_out, "w", header=header)

        for record in vcf_in:
            vcf_out.write(record)

        vcf_out.close()
        vcf_in.close()

        self.complete_check(fn_in, fn_out)
Ejemplo n.º 19
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 def setUp(self):
     self.tmpfilename = get_temp_filename(suffix="vcf")
     shutil.copyfile(self.filename, self.tmpfilename)
     pysam.tabix_index(self.tmpfilename, preset="vcf")
Ejemplo n.º 20
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 def setUp(self):
     self.tmpfilename = get_temp_filename(suffix="vcf")
     shutil.copyfile(self.filename, self.tmpfilename)
     pysam.tabix_index(self.tmpfilename, preset="vcf")
Ejemplo n.º 21
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    def setUp(self):

        self.tmpfilename = get_temp_filename(suffix="gtf.gz")
        shutil.copyfile(self.filename, self.tmpfilename)
Ejemplo n.º 22
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 def setUp(self):
     self.tmpfilename = get_temp_filename(suffix="gtf")
     with gzip.open(self.filename, "rb") as infile, \
             open(self.tmpfilename, "wb") as outfile:
         outfile.write(infile.read())
Ejemplo n.º 23
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    def setUp(self):

        self.tmpfilename = get_temp_filename(suffix="gtf.gz")
        shutil.copyfile(self.filename, self.tmpfilename)
Ejemplo n.º 24
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 def setUp(self):
     self.tmpfilename = get_temp_filename(suffix="gtf")
     with gzip.open(self.filename, "rb") as infile, \
             open(self.tmpfilename, "wb") as outfile:
         outfile.write(infile.read())