I’ve just finished writing up an example for the Biopython Tutorial of the new GenomeDiagram functionality added in Biopython 1.59. […]
Cross-links in GenomeDiagram
March 2nd, 2012 by PeterChromosome Diagrams in Biopython
October 28th, 2011 by PeterOne of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. […]
Illumina FASTQ files – Read Segment Quality Control Indicator
April 30th, 2010 by PeterIn another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores […]
Partial sequence files with Biopython
April 27th, 2010 by PeterThis is another blog post to highlight one of the neat tricks you’ll be able to do with Biopython 1.54 […]
Interleaving paired FASTQ files with Biopython
December 14th, 2009 by PeterThis post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ […]
Working with FASTQ files in Biopython when speed matters
September 25th, 2009 by PeterBiopython’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.
Simpler, optimized format conversion with Biopython
September 22nd, 2009 by davidwIn 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.
Indexing sequence files with Biopython
September 21st, 2009 by PeterThe 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.
Clever tricks with NCBI Entrez EInfo (& Biopython)
June 21st, 2009 by PeterConstructing complicated Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help. This can tell you all the searchable fields available for each of the Entrez databases.
Introducing (and expanding) the Biopython Cookbook
April 29th, 2009 by davidwHi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea […]
HOWTO automate tree drawing
June 15th, 2007 by Jason StajichI updated the Trees HowTo with some code demonstrating how to automatically generate postscript trees from newick or nexus tree […]