# 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 + ++++))'''')(''')$!$''')''''(+.''$!$))))+)))''''''' 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 Note these examples only show the first 50 bases to keep the output short. """ from collections.abc import Iterator from Bio.SeqRecord import SeqRecord from Bio.Sequencing import Phd from .Interfaces import _IOSource from .Interfaces import _TextIOSource from .Interfaces import SequenceIterator from .Interfaces import SequenceWriter from .QualityIO import _get_phred_quality class PhdIterator(SequenceIterator): """Parser for PHD files.""" modes = "t" def __init__(self, source: _TextIOSource) -> None: """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. """ super().__init__(source, fmt="PHD") def __next__(self): phd_record = Phd._read(self.stream) if phd_record is None: raise StopIteration # 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 reuse 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 return seq_record class PhdWriter(SequenceWriter): """Class to write Phd format files.""" modes = "t" 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 = _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()