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
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
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
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)
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)
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)
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)
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)