Esempio n. 1
0
def PhdIterator(handle):
    """Returns SeqRecord objects from a PHD file.

    This uses the Bio.Sequencing.Phd module to do the hard work.
    """
    phd_records = Phd.parse(handle)
    for phd_record in phd_records:
        # Convert the PHY record into a SeqRecord...
        # The "filename" can contain spaces, e.g. 'HWI-EAS94_4_1_1_602_99 1'
        # from unit test example file phd_solexa.
        # This will cause problems if used as the record identifier
        # (e.g. output for FASTQ format).
        name = phd_record.file_name.split(None, 1)[0]
        seq_record = SeqRecord(phd_record.seq,
                               id=name, name=name,
                               description=phd_record.file_name)
        # Just re-use the comments dictionary as the SeqRecord's annotations
        seq_record.annotations = phd_record.comments
        # And store the qualities and peak locations as per-letter-annotation
        seq_record.letter_annotations["phred_quality"] = \
            [int(site[1]) for site in phd_record.sites]
        try:
            seq_record.letter_annotations["peak_location"] = \
                [int(site[2]) for site in phd_record.sites]
        except IndexError:
            # peak locations are not always there according to
            # David Gordon (the Consed author)
            pass
        yield seq_record
Esempio n. 2
0
def PhdIterator(handle):
    """Returns SeqRecord objects from a PHD file.

    This uses the Bio.Sequencing.Phd module to do the hard work.
    """
    phd_records = Phd.parse(handle)
    for phd_record in phd_records:
        # Convert the PHY record into a SeqRecord...
        # The "filename" can contain spaces, e.g. 'HWI-EAS94_4_1_1_602_99 1'
        # from unit test example file phd_solexa.
        # This will cause problems if used as the record identifier
        # (e.g. output for FASTQ format).
        name = phd_record.file_name.split(None, 1)[0]
        seq_record = SeqRecord(phd_record.seq,
                               id=name,
                               name=name,
                               description=phd_record.file_name)
        # Just re-use the comments dictionary as the SeqRecord's annotations
        seq_record.annotations = phd_record.comments
        # And store the qualities and peak locations as per-letter-annotation
        seq_record.letter_annotations["phred_quality"] = \
            [int(site[1]) for site in phd_record.sites]
        try:
            seq_record.letter_annotations["peak_location"] = \
                [int(site[2]) for site in phd_record.sites]
        except IndexError:
            # peak locations are not always there according to
            # David Gordon (the Consed author)
            pass
        yield seq_record
Esempio n. 3
0
def PhdIterator(handle) :
    """Returns SeqRecord objects from a PHD file.

    This uses the Bio.Sequencing.Phy module to do the hard work.
    """

    phd_records = Phd.parse(handle)
    for phd_record in phd_records:
        #Convert the PHY record into a SeqRecord...
        seq_record = SeqRecord(phd_record.seq,
                               id = phd_record.file_name,
                               name = phd_record.file_name)
        #Just re-use the comments dictionary as the SeqRecord's annotations
        seq_record.annotations = phd_record.comments
        yield seq_record 
Esempio n. 4
0
 def test_check_record_parser(self):
     """Test phd1 file in detail."""
     records = Phd.parse(self.handle)
     # Record 1
     record = records.next()
     self.assertEqual(record.file_name, "34_222_(80-A03-19).b.ab1")
     self.assertEqual(record.comments['abi_thumbprint'], 0)
     self.assertEqual(record.comments['call_method'], "phred")
     self.assertEqual(record.comments['chem'], "term")
     self.assertEqual(record.comments['chromat_file'],
                      "34_222_(80-A03-19).b.ab1")
     self.assertEqual(record.comments['dye'], "big")
     self.assertEqual(record.comments['phred_version'], "0.020425.c")
     self.assertEqual(record.comments['quality_levels'], 99)
     self.assertEqual(record.comments['time'], "Fri Feb 13 09:16:11 2004")
     self.assertEqual(record.comments['trace_array_max_index'], 10867)
     self.assertEqual(record.comments['trace_array_min_index'], 0)
     self.assertAlmostEqual(record.comments['trace_peak_area_ratio'],
                            0.1467)
     self.assertEqual(record.comments['trim'][0], 3)
     self.assertEqual(record.comments['trim'][1], 391)
     self.assertAlmostEqual(record.comments['trim'][2], 0.05)
     center = len(record.sites) // 2
     self.assertEqual(record.sites[0], ('c', '9', '6'))
     self.assertEqual(record.sites[1], ('t', '9', '18'))
     self.assertEqual(record.sites[2], ('c', '10', '26'))
     self.assertEqual(record.sites[3], ('c', '19', '38'))
     self.assertEqual(record.sites[4], ('g', '22', '49'))
     self.assertEqual(record.sites[5], ('t', '37', '65'))
     self.assertEqual(record.sites[6], ('c', '28', '76'))
     self.assertEqual(record.sites[7], ('g', '28', '87'))
     self.assertEqual(record.sites[8], ('g', '24', '100'))
     self.assertEqual(record.sites[9], ('a', '22', '108'))
     self.assertEqual(record.sites[center - 5], ('c', '11', '5259'))
     self.assertEqual(record.sites[center - 4], ('c', '11', '5273'))
     self.assertEqual(record.sites[center - 3], ('t', '9', '5286'))
     self.assertEqual(record.sites[center - 2], ('g', '10', '5300'))
     self.assertEqual(record.sites[center - 1], ('a', '10', '5316'))
     self.assertEqual(record.sites[center], ('t', '8', '5323'))
     self.assertEqual(record.sites[center + 1], ('c', '8', '5343'))
     self.assertEqual(record.sites[center + 2], ('g', '8', '5352'))
     self.assertEqual(record.sites[center + 3], ('c', '8', '5366'))
     self.assertEqual(record.sites[center + 4], ('c', '8', '5378'))
     self.assertEqual(record.sites[-10], ('c', '8', '10756'))
     self.assertEqual(record.sites[-9], ('c', '8', '10764'))
     self.assertEqual(record.sites[-8], ('a', '8', '10769'))
     self.assertEqual(record.sites[-7], ('a', '8', '10788'))
     self.assertEqual(record.sites[-6], ('a', '8', '10803'))
     self.assertEqual(record.sites[-5], ('g', '10', '10816'))
     self.assertEqual(record.sites[-4], ('c', '11', '10826'))
     self.assertEqual(record.sites[-3], ('g', '11', '10840'))
     self.assertEqual(record.sites[-2], ('t', '11', '10855'))
     self.assertEqual(record.sites[-1], ('g', '11', '10864'))
     self.assertEqual(str(record.seq)[:10], 'ctccgtcgga')
     self.assertEqual(str(record.seq)[-10:], 'ccaaagcgtg')
     self.assertEqual(str(record.seq_trimmed)[:10], 'cgtcggaaca')
     self.assertEqual(str(record.seq_trimmed)[-10:], 'tatttcggag')
     # Record 2
     record = records.next()
     center = len(record.sites) // 2
     self.assertEqual(record.file_name, "425_103_(81-A03-19).g.ab1")
     self.assertEqual(record.comments['abi_thumbprint'], 0)
     self.assertEqual(record.comments['call_method'], 'phred')
     self.assertEqual(record.comments['chem'], 'term')
     self.assertEqual(record.comments['chromat_file'],
                      '425_103_(81-A03-19).g.ab1')
     self.assertEqual(record.comments['dye'], 'big')
     self.assertEqual(record.comments['phred_version'], '0.020425.c')
     self.assertEqual(record.comments['quality_levels'], 99)
     self.assertEqual(record.comments['time'], 'Tue Feb 17 10:31:15 2004')
     self.assertEqual(record.comments['trace_array_max_index'], 10606)
     self.assertEqual(record.comments['trace_array_min_index'], 0)
     self.assertAlmostEqual(record.comments['trace_peak_area_ratio'],
                            0.0226)
     self.assertEqual(record.comments['trim'][0], 10)
     self.assertEqual(record.comments['trim'][1], 432)
     self.assertAlmostEqual(record.comments['trim'][2], 0.05)
     self.assertEqual(record.sites[0], ('c', '14', '3'))
     self.assertEqual(record.sites[1], ('g', '17', '11'))
     self.assertEqual(record.sites[2], ('g', '22', '23'))
     self.assertEqual(record.sites[3], ('g', '10', '35'))
     self.assertEqual(record.sites[4], ('a', '10', '53'))
     self.assertEqual(record.sites[5], ('t', '10', '68'))
     self.assertEqual(record.sites[6], ('c', '15', '75'))
     self.assertEqual(record.sites[7], ('c', '8', '85'))
     self.assertEqual(record.sites[8], ('c', '8', '94'))
     self.assertEqual(record.sites[9], ('a', '9', '115'))
     self.assertEqual(record.sites[center - 5], ('c', '33', '5140'))
     self.assertEqual(record.sites[center - 4], ('c', '28', '5156'))
     self.assertEqual(record.sites[center - 3], ('g', '25', '5167'))
     self.assertEqual(record.sites[center - 2], ('c', '28', '5178'))
     self.assertEqual(record.sites[center - 1], ('c', '18', '5193'))
     self.assertEqual(record.sites[center], ('a', '16', '5204'))
     self.assertEqual(record.sites[center + 1], ('a', '15', '5213'))
     self.assertEqual(record.sites[center + 2], ('a', '10', '5230'))
     self.assertEqual(record.sites[center + 3], ('a', '10', '5242'))
     self.assertEqual(record.sites[center + 4], ('t', '8', '5249'))
     self.assertEqual(record.sites[-10], ('c', '8', '10489'))
     self.assertEqual(record.sites[-9], ('c', '8', '10503'))
     self.assertEqual(record.sites[-8], ('c', '8', '10514'))
     self.assertEqual(record.sites[-7], ('a', '8', '10516'))
     self.assertEqual(record.sites[-6], ('g', '8', '10530'))
     self.assertEqual(record.sites[-5], ('c', '8', '10550'))
     self.assertEqual(record.sites[-4], ('c', '10', '10566'))
     self.assertEqual(record.sites[-3], ('a', '8', '10574'))
     self.assertEqual(record.sites[-2], ('a', '7', '10584'))
     self.assertEqual(record.sites[-1], ('g', '7', '10599'))
     self.assertEqual(str(record.seq)[:10], 'cgggatccca')
     self.assertEqual(str(record.seq)[-10:], 'cccagccaag')
     self.assertEqual(str(record.seq_trimmed)[:10], 'cctgatccga')
     self.assertEqual(str(record.seq_trimmed)[-10:], 'ggggccgcca')
     # Record 3
     record = records.next()
     center = len(record.sites) // 2
     self.assertEqual(record.file_name, '425_7_(71-A03-19).b.ab1')
     self.assertEqual(record.comments['abi_thumbprint'], 0)
     self.assertEqual(record.comments['call_method'], 'phred')
     self.assertEqual(record.comments['chem'], 'term')
     self.assertEqual(record.comments['chromat_file'],
                      '425_7_(71-A03-19).b.ab1')
     self.assertEqual(record.comments['dye'], 'big')
     self.assertEqual(record.comments['phred_version'], '0.020425.c')
     self.assertEqual(record.comments['quality_levels'], 99)
     self.assertEqual(record.comments['time'], 'Thu Jan 29 11:46:14 2004')
     self.assertEqual(record.comments['trace_array_max_index'], 9513)
     self.assertEqual(record.comments['trace_array_min_index'], 0)
     self.assertAlmostEqual(record.comments['trace_peak_area_ratio'], 100.0)
     self.assertEqual(record.comments['trim'][0], -1)
     self.assertEqual(record.comments['trim'][1], -1)
     self.assertEqual(record.comments['trim'][2], 0.05)
     self.assertEqual(record.sites[0], ('a', '10', '7'))
     self.assertEqual(record.sites[1], ('c', '10', '13'))
     self.assertEqual(record.sites[2], ('a', '10', '21'))
     self.assertEqual(record.sites[3], ('t', '10', '28'))
     self.assertEqual(record.sites[4], ('a', '8', '33'))
     self.assertEqual(record.sites[5], ('a', '8', '40'))
     self.assertEqual(record.sites[6], ('a', '6', '50'))
     self.assertEqual(record.sites[7], ('t', '6', '53'))
     self.assertEqual(record.sites[8], ('c', '6', '66'))
     self.assertEqual(record.sites[9], ('a', '6', '68'))
     self.assertEqual(record.sites[center - 5], ('a', '6', '4728'))
     self.assertEqual(record.sites[center - 4], ('t', '10', '4737'))
     self.assertEqual(record.sites[center - 3], ('a', '10', '4746'))
     self.assertEqual(record.sites[center - 2], ('a', '8', '4756'))
     self.assertEqual(record.sites[center - 1], ('t', '8', '4759'))
     self.assertEqual(record.sites[center], ('t', '8', '4768'))
     self.assertEqual(record.sites[center + 1], ('a', '8', '4775'))
     self.assertEqual(record.sites[center + 2], ('g', '10', '4783'))
     self.assertEqual(record.sites[center + 3], ('t', '8', '4788'))
     self.assertEqual(record.sites[center + 4], ('g', '8', '4794'))
     self.assertEqual(record.sites[-10], ('a', '8', '9445'))
     self.assertEqual(record.sites[-9], ('t', '6', '9453'))
     self.assertEqual(record.sites[-8], ('c', '6', '9462'))
     self.assertEqual(record.sites[-7], ('t', '6', '9465'))
     self.assertEqual(record.sites[-6], ('g', '6', '9478'))
     self.assertEqual(record.sites[-5], ('c', '6', '9483'))
     self.assertEqual(record.sites[-4], ('t', '6', '9485'))
     self.assertEqual(record.sites[-3], ('t', '8', '9495'))
     self.assertEqual(record.sites[-2], ('t', '3', '9504'))
     self.assertEqual(record.sites[-1], ('n', '0', '9511'))
     self.assertEqual(str(record.seq)[:10], 'acataaatca')
     self.assertEqual(str(record.seq)[-10:], 'atctgctttn')
     # Make sure that no further records are found
     self.assertRaises(StopIteration, records.next)
Esempio n. 5
0
 def test_check_record_parser(self):
     """Test phd1 file in detail."""
     records = Phd.parse(self.handle)
     # Record 1
     record = next(records)
     self.assertEqual(record.file_name, "34_222_(80-A03-19).b.ab1")
     self.assertEqual(record.comments["abi_thumbprint"], 0)
     self.assertEqual(record.comments["call_method"], "phred")
     self.assertEqual(record.comments["chem"], "term")
     self.assertEqual(record.comments["chromat_file"],
                      "34_222_(80-A03-19).b.ab1")
     self.assertEqual(record.comments["dye"], "big")
     self.assertEqual(record.comments["phred_version"], "0.020425.c")
     self.assertEqual(record.comments["quality_levels"], 99)
     self.assertEqual(record.comments["time"], "Fri Feb 13 09:16:11 2004")
     self.assertEqual(record.comments["trace_array_max_index"], 10867)
     self.assertEqual(record.comments["trace_array_min_index"], 0)
     self.assertAlmostEqual(record.comments["trace_peak_area_ratio"],
                            0.1467)
     self.assertEqual(record.comments["trim"][0], 3)
     self.assertEqual(record.comments["trim"][1], 391)
     self.assertAlmostEqual(record.comments["trim"][2], 0.05)
     center = len(record.sites) // 2
     self.assertEqual(record.sites[0], ("c", "9", "6"))
     self.assertEqual(record.sites[1], ("t", "9", "18"))
     self.assertEqual(record.sites[2], ("c", "10", "26"))
     self.assertEqual(record.sites[3], ("c", "19", "38"))
     self.assertEqual(record.sites[4], ("g", "22", "49"))
     self.assertEqual(record.sites[5], ("t", "37", "65"))
     self.assertEqual(record.sites[6], ("c", "28", "76"))
     self.assertEqual(record.sites[7], ("g", "28", "87"))
     self.assertEqual(record.sites[8], ("g", "24", "100"))
     self.assertEqual(record.sites[9], ("a", "22", "108"))
     self.assertEqual(record.sites[center - 5], ("c", "11", "5259"))
     self.assertEqual(record.sites[center - 4], ("c", "11", "5273"))
     self.assertEqual(record.sites[center - 3], ("t", "9", "5286"))
     self.assertEqual(record.sites[center - 2], ("g", "10", "5300"))
     self.assertEqual(record.sites[center - 1], ("a", "10", "5316"))
     self.assertEqual(record.sites[center], ("t", "8", "5323"))
     self.assertEqual(record.sites[center + 1], ("c", "8", "5343"))
     self.assertEqual(record.sites[center + 2], ("g", "8", "5352"))
     self.assertEqual(record.sites[center + 3], ("c", "8", "5366"))
     self.assertEqual(record.sites[center + 4], ("c", "8", "5378"))
     self.assertEqual(record.sites[-10], ("c", "8", "10756"))
     self.assertEqual(record.sites[-9], ("c", "8", "10764"))
     self.assertEqual(record.sites[-8], ("a", "8", "10769"))
     self.assertEqual(record.sites[-7], ("a", "8", "10788"))
     self.assertEqual(record.sites[-6], ("a", "8", "10803"))
     self.assertEqual(record.sites[-5], ("g", "10", "10816"))
     self.assertEqual(record.sites[-4], ("c", "11", "10826"))
     self.assertEqual(record.sites[-3], ("g", "11", "10840"))
     self.assertEqual(record.sites[-2], ("t", "11", "10855"))
     self.assertEqual(record.sites[-1], ("g", "11", "10864"))
     self.assertEqual(str(record.seq)[:10], "ctccgtcgga")
     self.assertEqual(str(record.seq)[-10:], "ccaaagcgtg")
     self.assertEqual(str(record.seq_trimmed)[:10], "cgtcggaaca")
     self.assertEqual(str(record.seq_trimmed)[-10:], "tatttcggag")
     # Record 2
     record = next(records)
     center = len(record.sites) // 2
     self.assertEqual(record.file_name, "425_103_(81-A03-19).g.ab1")
     self.assertEqual(record.comments["abi_thumbprint"], 0)
     self.assertEqual(record.comments["call_method"], "phred")
     self.assertEqual(record.comments["chem"], "term")
     self.assertEqual(record.comments["chromat_file"],
                      "425_103_(81-A03-19).g.ab1")
     self.assertEqual(record.comments["dye"], "big")
     self.assertEqual(record.comments["phred_version"], "0.020425.c")
     self.assertEqual(record.comments["quality_levels"], 99)
     self.assertEqual(record.comments["time"], "Tue Feb 17 10:31:15 2004")
     self.assertEqual(record.comments["trace_array_max_index"], 10606)
     self.assertEqual(record.comments["trace_array_min_index"], 0)
     self.assertAlmostEqual(record.comments["trace_peak_area_ratio"],
                            0.0226)
     self.assertEqual(record.comments["trim"][0], 10)
     self.assertEqual(record.comments["trim"][1], 432)
     self.assertAlmostEqual(record.comments["trim"][2], 0.05)
     self.assertEqual(record.sites[0], ("c", "14", "3"))
     self.assertEqual(record.sites[1], ("g", "17", "11"))
     self.assertEqual(record.sites[2], ("g", "22", "23"))
     self.assertEqual(record.sites[3], ("g", "10", "35"))
     self.assertEqual(record.sites[4], ("a", "10", "53"))
     self.assertEqual(record.sites[5], ("t", "10", "68"))
     self.assertEqual(record.sites[6], ("c", "15", "75"))
     self.assertEqual(record.sites[7], ("c", "8", "85"))
     self.assertEqual(record.sites[8], ("c", "8", "94"))
     self.assertEqual(record.sites[9], ("a", "9", "115"))
     self.assertEqual(record.sites[center - 5], ("c", "33", "5140"))
     self.assertEqual(record.sites[center - 4], ("c", "28", "5156"))
     self.assertEqual(record.sites[center - 3], ("g", "25", "5167"))
     self.assertEqual(record.sites[center - 2], ("c", "28", "5178"))
     self.assertEqual(record.sites[center - 1], ("c", "18", "5193"))
     self.assertEqual(record.sites[center], ("a", "16", "5204"))
     self.assertEqual(record.sites[center + 1], ("a", "15", "5213"))
     self.assertEqual(record.sites[center + 2], ("a", "10", "5230"))
     self.assertEqual(record.sites[center + 3], ("a", "10", "5242"))
     self.assertEqual(record.sites[center + 4], ("t", "8", "5249"))
     self.assertEqual(record.sites[-10], ("c", "8", "10489"))
     self.assertEqual(record.sites[-9], ("c", "8", "10503"))
     self.assertEqual(record.sites[-8], ("c", "8", "10514"))
     self.assertEqual(record.sites[-7], ("a", "8", "10516"))
     self.assertEqual(record.sites[-6], ("g", "8", "10530"))
     self.assertEqual(record.sites[-5], ("c", "8", "10550"))
     self.assertEqual(record.sites[-4], ("c", "10", "10566"))
     self.assertEqual(record.sites[-3], ("a", "8", "10574"))
     self.assertEqual(record.sites[-2], ("a", "7", "10584"))
     self.assertEqual(record.sites[-1], ("g", "7", "10599"))
     self.assertEqual(str(record.seq)[:10], "cgggatccca")
     self.assertEqual(str(record.seq)[-10:], "cccagccaag")
     self.assertEqual(str(record.seq_trimmed)[:10], "cctgatccga")
     self.assertEqual(str(record.seq_trimmed)[-10:], "ggggccgcca")
     # Record 3
     record = next(records)
     center = len(record.sites) // 2
     self.assertEqual(record.file_name, "425_7_(71-A03-19).b.ab1")
     self.assertEqual(record.comments["abi_thumbprint"], 0)
     self.assertEqual(record.comments["call_method"], "phred")
     self.assertEqual(record.comments["chem"], "term")
     self.assertEqual(record.comments["chromat_file"],
                      "425_7_(71-A03-19).b.ab1")
     self.assertEqual(record.comments["dye"], "big")
     self.assertEqual(record.comments["phred_version"], "0.020425.c")
     self.assertEqual(record.comments["quality_levels"], 99)
     self.assertEqual(record.comments["time"], "Thu Jan 29 11:46:14 2004")
     self.assertEqual(record.comments["trace_array_max_index"], 9513)
     self.assertEqual(record.comments["trace_array_min_index"], 0)
     self.assertAlmostEqual(record.comments["trace_peak_area_ratio"], 100.0)
     self.assertEqual(record.comments["trim"][0], -1)
     self.assertEqual(record.comments["trim"][1], -1)
     self.assertEqual(record.comments["trim"][2], 0.05)
     self.assertEqual(record.sites[0], ("a", "10", "7"))
     self.assertEqual(record.sites[1], ("c", "10", "13"))
     self.assertEqual(record.sites[2], ("a", "10", "21"))
     self.assertEqual(record.sites[3], ("t", "10", "28"))
     self.assertEqual(record.sites[4], ("a", "8", "33"))
     self.assertEqual(record.sites[5], ("a", "8", "40"))
     self.assertEqual(record.sites[6], ("a", "6", "50"))
     self.assertEqual(record.sites[7], ("t", "6", "53"))
     self.assertEqual(record.sites[8], ("c", "6", "66"))
     self.assertEqual(record.sites[9], ("a", "6", "68"))
     self.assertEqual(record.sites[center - 5], ("a", "6", "4728"))
     self.assertEqual(record.sites[center - 4], ("t", "10", "4737"))
     self.assertEqual(record.sites[center - 3], ("a", "10", "4746"))
     self.assertEqual(record.sites[center - 2], ("a", "8", "4756"))
     self.assertEqual(record.sites[center - 1], ("t", "8", "4759"))
     self.assertEqual(record.sites[center], ("t", "8", "4768"))
     self.assertEqual(record.sites[center + 1], ("a", "8", "4775"))
     self.assertEqual(record.sites[center + 2], ("g", "10", "4783"))
     self.assertEqual(record.sites[center + 3], ("t", "8", "4788"))
     self.assertEqual(record.sites[center + 4], ("g", "8", "4794"))
     self.assertEqual(record.sites[-10], ("a", "8", "9445"))
     self.assertEqual(record.sites[-9], ("t", "6", "9453"))
     self.assertEqual(record.sites[-8], ("c", "6", "9462"))
     self.assertEqual(record.sites[-7], ("t", "6", "9465"))
     self.assertEqual(record.sites[-6], ("g", "6", "9478"))
     self.assertEqual(record.sites[-5], ("c", "6", "9483"))
     self.assertEqual(record.sites[-4], ("t", "6", "9485"))
     self.assertEqual(record.sites[-3], ("t", "8", "9495"))
     self.assertEqual(record.sites[-2], ("t", "3", "9504"))
     self.assertEqual(record.sites[-1], ("n", "0", "9511"))
     self.assertEqual(str(record.seq)[:10], "acataaatca")
     self.assertEqual(str(record.seq)[-10:], "atctgctttn")
     # Make sure that no further records are found
     self.assertRaises(StopIteration, next, records)
Esempio n. 6
0
 def test_check_record_parser(self):
     """Test phd1 file in detail."""
     records = Phd.parse(self.handle)
     # Record 1
     record = next(records)
     self.assertEqual(record.file_name, "34_222_(80-A03-19).b.ab1")
     self.assertEqual(record.comments['abi_thumbprint'], 0)
     self.assertEqual(record.comments['call_method'], "phred")
     self.assertEqual(record.comments['chem'], "term")
     self.assertEqual(record.comments['chromat_file'], "34_222_(80-A03-19).b.ab1")
     self.assertEqual(record.comments['dye'], "big")
     self.assertEqual(record.comments['phred_version'], "0.020425.c")
     self.assertEqual(record.comments['quality_levels'], 99)
     self.assertEqual(record.comments['time'], "Fri Feb 13 09:16:11 2004")
     self.assertEqual(record.comments['trace_array_max_index'], 10867)
     self.assertEqual(record.comments['trace_array_min_index'], 0)
     self.assertAlmostEqual(record.comments['trace_peak_area_ratio'], 0.1467)
     self.assertEqual(record.comments['trim'][0], 3)
     self.assertEqual(record.comments['trim'][1], 391)
     self.assertAlmostEqual(record.comments['trim'][2], 0.05)
     center = len(record.sites)//2
     self.assertEqual(record.sites[0], ('c', '9', '6'))
     self.assertEqual(record.sites[1], ('t', '9', '18'))
     self.assertEqual(record.sites[2], ('c', '10', '26'))
     self.assertEqual(record.sites[3], ('c', '19', '38'))
     self.assertEqual(record.sites[4], ('g', '22', '49'))
     self.assertEqual(record.sites[5], ('t', '37', '65'))
     self.assertEqual(record.sites[6], ('c', '28', '76'))
     self.assertEqual(record.sites[7], ('g', '28', '87'))
     self.assertEqual(record.sites[8], ('g', '24', '100'))
     self.assertEqual(record.sites[9], ('a', '22', '108'))
     self.assertEqual(record.sites[center-5], ('c', '11', '5259'))
     self.assertEqual(record.sites[center-4], ('c', '11', '5273'))
     self.assertEqual(record.sites[center-3], ('t', '9', '5286'))
     self.assertEqual(record.sites[center-2], ('g', '10', '5300'))
     self.assertEqual(record.sites[center-1], ('a', '10', '5316'))
     self.assertEqual(record.sites[center], ('t', '8', '5323'))
     self.assertEqual(record.sites[center+1], ('c', '8', '5343'))
     self.assertEqual(record.sites[center+2], ('g', '8', '5352'))
     self.assertEqual(record.sites[center+3], ('c', '8', '5366'))
     self.assertEqual(record.sites[center+4], ('c', '8', '5378'))
     self.assertEqual(record.sites[-10], ('c', '8', '10756'))
     self.assertEqual(record.sites[-9], ('c', '8', '10764'))
     self.assertEqual(record.sites[-8], ('a', '8', '10769'))
     self.assertEqual(record.sites[-7], ('a', '8', '10788'))
     self.assertEqual(record.sites[-6], ('a', '8', '10803'))
     self.assertEqual(record.sites[-5], ('g', '10', '10816'))
     self.assertEqual(record.sites[-4], ('c', '11', '10826'))
     self.assertEqual(record.sites[-3], ('g', '11', '10840'))
     self.assertEqual(record.sites[-2], ('t', '11', '10855'))
     self.assertEqual(record.sites[-1], ('g', '11', '10864'))
     self.assertEqual(str(record.seq)[:10], 'ctccgtcgga')
     self.assertEqual(str(record.seq)[-10:], 'ccaaagcgtg')
     self.assertEqual(str(record.seq_trimmed)[:10], 'cgtcggaaca')
     self.assertEqual(str(record.seq_trimmed)[-10:], 'tatttcggag')
     # Record 2
     record = next(records)
     center = len(record.sites)//2
     self.assertEqual(record.file_name, "425_103_(81-A03-19).g.ab1")
     self.assertEqual(record.comments['abi_thumbprint'], 0)
     self.assertEqual(record.comments['call_method'], 'phred')
     self.assertEqual(record.comments['chem'], 'term')
     self.assertEqual(record.comments['chromat_file'], '425_103_(81-A03-19).g.ab1')
     self.assertEqual(record.comments['dye'], 'big')
     self.assertEqual(record.comments['phred_version'], '0.020425.c')
     self.assertEqual(record.comments['quality_levels'], 99)
     self.assertEqual(record.comments['time'], 'Tue Feb 17 10:31:15 2004')
     self.assertEqual(record.comments['trace_array_max_index'], 10606)
     self.assertEqual(record.comments['trace_array_min_index'], 0)
     self.assertAlmostEqual(record.comments['trace_peak_area_ratio'], 0.0226)
     self.assertEqual(record.comments['trim'][0], 10)
     self.assertEqual(record.comments['trim'][1], 432)
     self.assertAlmostEqual(record.comments['trim'][2], 0.05)
     self.assertEqual(record.sites[0], ('c', '14', '3'))
     self.assertEqual(record.sites[1], ('g', '17', '11'))
     self.assertEqual(record.sites[2], ('g', '22', '23'))
     self.assertEqual(record.sites[3], ('g', '10', '35'))
     self.assertEqual(record.sites[4], ('a', '10', '53'))
     self.assertEqual(record.sites[5], ('t', '10', '68'))
     self.assertEqual(record.sites[6], ('c', '15', '75'))
     self.assertEqual(record.sites[7], ('c', '8', '85'))
     self.assertEqual(record.sites[8], ('c', '8', '94'))
     self.assertEqual(record.sites[9], ('a', '9', '115'))
     self.assertEqual(record.sites[center-5], ('c', '33', '5140'))
     self.assertEqual(record.sites[center-4], ('c', '28', '5156'))
     self.assertEqual(record.sites[center-3], ('g', '25', '5167'))
     self.assertEqual(record.sites[center-2], ('c', '28', '5178'))
     self.assertEqual(record.sites[center-1], ('c', '18', '5193'))
     self.assertEqual(record.sites[center], ('a', '16', '5204'))
     self.assertEqual(record.sites[center+1], ('a', '15', '5213'))
     self.assertEqual(record.sites[center+2], ('a', '10', '5230'))
     self.assertEqual(record.sites[center+3], ('a', '10', '5242'))
     self.assertEqual(record.sites[center+4], ('t', '8', '5249'))
     self.assertEqual(record.sites[-10], ('c', '8', '10489'))
     self.assertEqual(record.sites[-9], ('c', '8', '10503'))
     self.assertEqual(record.sites[-8], ('c', '8', '10514'))
     self.assertEqual(record.sites[-7], ('a', '8', '10516'))
     self.assertEqual(record.sites[-6], ('g', '8', '10530'))
     self.assertEqual(record.sites[-5], ('c', '8', '10550'))
     self.assertEqual(record.sites[-4], ('c', '10', '10566'))
     self.assertEqual(record.sites[-3], ('a', '8', '10574'))
     self.assertEqual(record.sites[-2], ('a', '7', '10584'))
     self.assertEqual(record.sites[-1], ('g', '7', '10599'))
     self.assertEqual(str(record.seq)[:10], 'cgggatccca')
     self.assertEqual(str(record.seq)[-10:], 'cccagccaag')
     self.assertEqual(str(record.seq_trimmed)[:10], 'cctgatccga')
     self.assertEqual(str(record.seq_trimmed)[-10:], 'ggggccgcca')
     # Record 3
     record = next(records)
     center = len(record.sites)//2
     self.assertEqual(record.file_name, '425_7_(71-A03-19).b.ab1')
     self.assertEqual(record.comments['abi_thumbprint'], 0)
     self.assertEqual(record.comments['call_method'], 'phred')
     self.assertEqual(record.comments['chem'], 'term')
     self.assertEqual(record.comments['chromat_file'], '425_7_(71-A03-19).b.ab1')
     self.assertEqual(record.comments['dye'], 'big')
     self.assertEqual(record.comments['phred_version'], '0.020425.c')
     self.assertEqual(record.comments['quality_levels'], 99)
     self.assertEqual(record.comments['time'], 'Thu Jan 29 11:46:14 2004')
     self.assertEqual(record.comments['trace_array_max_index'], 9513)
     self.assertEqual(record.comments['trace_array_min_index'], 0)
     self.assertAlmostEqual(record.comments['trace_peak_area_ratio'], 100.0)
     self.assertEqual(record.comments['trim'][0], -1)
     self.assertEqual(record.comments['trim'][1], -1)
     self.assertEqual(record.comments['trim'][2], 0.05)
     self.assertEqual(record.sites[0], ('a', '10', '7'))
     self.assertEqual(record.sites[1], ('c', '10', '13'))
     self.assertEqual(record.sites[2], ('a', '10', '21'))
     self.assertEqual(record.sites[3], ('t', '10', '28'))
     self.assertEqual(record.sites[4], ('a', '8', '33'))
     self.assertEqual(record.sites[5], ('a', '8', '40'))
     self.assertEqual(record.sites[6], ('a', '6', '50'))
     self.assertEqual(record.sites[7], ('t', '6', '53'))
     self.assertEqual(record.sites[8], ('c', '6', '66'))
     self.assertEqual(record.sites[9], ('a', '6', '68'))
     self.assertEqual(record.sites[center-5], ('a', '6', '4728'))
     self.assertEqual(record.sites[center-4], ('t', '10', '4737'))
     self.assertEqual(record.sites[center-3], ('a', '10', '4746'))
     self.assertEqual(record.sites[center-2], ('a', '8', '4756'))
     self.assertEqual(record.sites[center-1], ('t', '8', '4759'))
     self.assertEqual(record.sites[center], ('t', '8', '4768'))
     self.assertEqual(record.sites[center+1], ('a', '8', '4775'))
     self.assertEqual(record.sites[center+2], ('g', '10', '4783'))
     self.assertEqual(record.sites[center+3], ('t', '8', '4788'))
     self.assertEqual(record.sites[center+4], ('g', '8', '4794'))
     self.assertEqual(record.sites[-10], ('a', '8', '9445'))
     self.assertEqual(record.sites[-9], ('t', '6', '9453'))
     self.assertEqual(record.sites[-8], ('c', '6', '9462'))
     self.assertEqual(record.sites[-7], ('t', '6', '9465'))
     self.assertEqual(record.sites[-6], ('g', '6', '9478'))
     self.assertEqual(record.sites[-5], ('c', '6', '9483'))
     self.assertEqual(record.sites[-4], ('t', '6', '9485'))
     self.assertEqual(record.sites[-3], ('t', '8', '9495'))
     self.assertEqual(record.sites[-2], ('t', '3', '9504'))
     self.assertEqual(record.sites[-1], ('n', '0', '9511'))
     self.assertEqual(str(record.seq)[:10], 'acataaatca')
     self.assertEqual(str(record.seq)[-10:], 'atctgctttn')
     # Make sure that no further records are found
     self.assertRaises(StopIteration, next, records)
Esempio n. 7
0
import pprint
from Bio.Sequencing import Phd
fn = '../../samples/phd1'
with open(fn) as fh:
    rp = Phd.read(fh)
# All the comments are in a dictionary
pprint.pprint(rp.comments)
# Sequence information
print('Sequence: %s' % rp.seq)
# Quality information for each base
print('Quality: %s' % rp.sites)
Esempio n. 8
0
import pprint
from Bio.Sequencing import Phd

fn = '../../samples/phd1'
with open(fn) as fh:
    rp = Phd.read(fh)
# All the comments are in a dictionary
pprint.pprint(rp.comments)
# Sequence information
print('Sequence: %s' % rp.seq)
# Quality information for each base
print('Quality: %s' % rp.sites)