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# Copyright 2008-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2009 by Cymon J. Cox. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support for the "phd" file format.
PHD files are output by PHRED and used by PHRAP and CONSED.
You are expected to use this module via the Bio.SeqIO functions, under the
format name "phd". See also the underlying Bio.Sequencing.Phd module.
For example, using Bio.SeqIO we can read in one of the example PHRED files
from the Biopython unit tests:
>>> from Bio import SeqIO
>>> for record in SeqIO.parse("Phd/phd1", "phd"):
... print(record.id)
... print("%s..." % record.seq[:10])
... print("%s..." % record.letter_annotations["phred_quality"][:10])
34_222_(80-A03-19).b.ab1
ctccgtcgga...
[9, 9, 10, 19, 22, 37, 28, 28, 24, 22]...
425_103_(81-A03-19).g.ab1
cgggatccca...
[14, 17, 22, 10, 10, 10, 15, 8, 8, 9]...
425_7_(71-A03-19).b.ab1
acataaatca...
[10, 10, 10, 10, 8, 8, 6, 6, 6, 6]...
Since PHRED files contain quality scores, you can save them as FASTQ or as
QUAL files, for example using Bio.SeqIO.write(...), or simply with the format
method of the SeqRecord object:
>>> print(record[:50].format("fastq"))
@425_7_(71-A03-19).b.ab1
acataaatcaaattactnaccaacacacaaaccngtctcgcgtagtggag
+
++++))'''')(''')$!$''')''''(+.''$!$))))+)))'''''''
<BLANKLINE>
Or,
>>> print(record[:50].format("qual"))
>425_7_(71-A03-19).b.ab1
10 10 10 10 8 8 6 6 6 6 8 7 6 6 6 8 3 0 3 6 6 6 8 6 6 6 6 7
10 13 6 6 3 0 3 8 8 8 8 10 8 8 8 6 6 6 6 6 6 6
<BLANKLINE>
Note these examples only show the first 50 bases to keep the output short.
"""
from Bio.SeqIO import QualityIO
from Bio.SeqRecord import SeqRecord
from Bio.Sequencing import Phd
from .Interfaces import SequenceWriter
def PhdIterator(source):
"""Return SeqRecord objects from a PHD file.
Arguments:
- source - input stream opened in text mode, or a path to a file
This uses the Bio.Sequencing.Phd module to do the hard work.
"""
phd_records = Phd.parse(source)
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
seq_record.annotations["molecule_type"] = "DNA"
# 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
# All done
class PhdWriter(SequenceWriter):
"""Class to write Phd format files."""
def __init__(self, handle):
"""Initialize the class."""
super().__init__(handle)
def write_record(self, record):
"""Write a single Phd record to the file."""
assert record.seq, "No sequence present in SeqRecord"
# This method returns the 'phred_quality' scores or converted
# 'solexa_quality' scores if present, else raises a value error
phred_qualities = QualityIO._get_phred_quality(record)
peak_locations = record.letter_annotations.get("peak_location")
if len(record.seq) != len(phred_qualities):
raise ValueError(
"Number of phd quality scores does not match length of sequence"
)
if peak_locations:
if len(record.seq) != len(peak_locations):
raise ValueError(
"Number of peak location scores does not "
"match length of sequence"
)
if None in phred_qualities:
raise ValueError("A quality value of None was found")
if record.description.startswith(f"{record.id} "):
title = record.description
else:
title = f"{record.id} {record.description}"
self.handle.write(f"BEGIN_SEQUENCE {self.clean(title)}\nBEGIN_COMMENT\n")
for annot in [k.lower() for k in Phd.CKEYWORDS]:
value = None
if annot == "trim":
if record.annotations.get("trim"):
value = "%s %s %.4f" % record.annotations["trim"]
elif annot == "trace_peak_area_ratio":
if record.annotations.get("trace_peak_area_ratio"):
value = f"{record.annotations['trace_peak_area_ratio']:.4f}"
else:
value = record.annotations.get(annot)
if value or value == 0:
self.handle.write(f"{annot.upper()}: {value}\n")
self.handle.write("END_COMMENT\nBEGIN_DNA\n")
for i, site in enumerate(record.seq):
if peak_locations:
self.handle.write(
"%s %i %i\n" % (site, round(phred_qualities[i]), peak_locations[i])
)
else:
self.handle.write("%s %i\n" % (site, round(phred_qualities[i])))
self.handle.write("END_DNA\nEND_SEQUENCE\n")
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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