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Category Archives: Code
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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BioPerl at GMOD Meeting 2010
BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just prior to the GMOD Meeting. Several items were covered on the agenda: In order to start addressing whole genome data with more lightweight objects, we are planning on … Continue reading
Posted in BioPerl, Code, Community, Development, OBF, OBF Projects
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BioRuby 1.4.0 released
We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to bug fixes and improvements. PhyloXML support: Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, … Continue reading
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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BioPerl interview in latest FLOSS Weekly
Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly. The interview is now available as an MP3 on the FLOSS Weekly website; several streaming versions (including podcast) are also available.
Posted in BioPerl, BOSC/ISMB, Code, Community, Development, General, OBF, OBF Projects
Tagged BioPerl
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First 1.6.1 alphas of BioPerl-Run, BioPerl-DB, BioPerl-Network
Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network They can also be downloaded from the BioPerl website: http://bioperl.org/DIST/RC/ This is … Continue reading