Module PhdIO
source code
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(open("Phd/phd1"), "phd"):
... print record.id
... print record.seq[:10], "..."
... print 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.
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__package__ = ' Bio.SeqIO '
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Returns SeqRecord objects from a PHD file.
This uses the Bio.Sequencing.Phd module to do the hard work.
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Run the Bio.SeqIO.PhdIO module's doctests.
This will try and locate the unit tests directory, and run the
doctests from there in order that the relative paths used in the examples
work.
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