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Tag Archives: Biopython
Biopython 1.55 beta released
We’ve just released a beta of Biopython 1.55 for user testing. Since Biopython 1.54 was released three months ago, we’ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of … Continue reading
Biopython 1.54 released
The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of … Continue reading
Posted in Biopython, Code, Community, Development, General, Google Summer of Code, OBF, OBF Projects
Tagged Biopython, release
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Illumina FASTQ files – Read Segment Quality Control Indicator
In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores – and a score of 2 has a special meaning, The Read Segment Quality Control Indicator (RSQCI, encoded as ‘B’). … Continue reading
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF, OBF Projects
Tagged Biopython, FASTQ
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Partial sequence files with Biopython
This is another blog post to highlight one of the neat tricks you’ll be able to do with Biopython 1.54 (which you can help test with the Biopython 1.54 beta release). It is often useful to be able to extract … Continue reading
Posted in Biopython, Blogroll, Code, Development, HOWTO, OBF, OBF Projects
Tagged Biopython
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Making Biopython SeqIO and AlignIO easier
One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles, but they will now also … Continue reading
Posted in Biopython, Blogroll, Code, Development, Documentation, OBF, OBF Projects
Tagged Biopython
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Biopython 1.54 beta released
A beta release for Biopython 1.54 is now available for download and testing.
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Sanger FASTQ format and the Solexa/Illumina variants
I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ … Continue reading
Posted in BioJava, BioPerl, Biopython, BioRuby, Blogroll, Community, Development, Documentation, General, OBF, OBF Projects
Tagged BioJava, BioPerl, Biopython, BioRuby, EMBOSS, FASTQ
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Biopython 1.53 released
We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months after the release of Biopython 1.52. This is our first release since migrating from CVS to git for source code … Continue reading
Interleaving paired FASTQ files with Biopython
This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ conversions & speeding up FASTQ).
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF Projects
Tagged Biopython, FASTQ
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Working with FASTQ files in Biopython when speed matters
Biopython’s SeqIO interface revolves around SeqRecord objects which can impose a speed penalty. For FASTQ files the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing. Working directly with the raw strings is less flexible, but much faster. Continue reading
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF Projects
Tagged Biopython, FASTQ
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