Category Archives: Documentation

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).

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BioPerl core 1.6.1 PPM available

BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be … Continue reading

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BioPerl 1.6.1 released

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here: Via CPAN: http://search.cpan.org/~cjfields/BioPerl-1.6.1/ Via the BioPerl website: http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip The PPM for Windows should also finally … Continue reading

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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

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Biopython CVS to git migration

Biopython has now moved from CVS to a git repository, hosted on github.com who kindly provide git hosting for open source projects free of charge. The BioRuby project have been using github for some time, so we are in good company. Continue reading

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Simpler, optimized format conversion with Biopython

In this post we’ll look at the new convert() function that both Bio.SeqIO and Bio.AlignIO will get in Biopython 1.52. This allows easier file conversion, and internally provides a mechanism for specific optimisations, such as for FASTQ conversions. Continue reading

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Indexing sequence files with Biopython

The forthcoming release of Biopython 1.52 will include a couple of nice improvements to the Bio.SeqIO module, and here we’re going to introduce the new index function. Continue reading

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