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.