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Archive for the ‘HOWTO’ Category

Illumina FASTQ files – Read Segment Quality Control Indicator

Friday, April 30th, 2010

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'). Hats off to Dr Torsten Seemann for raising awareness of this ...

Partial sequence files with Biopython

Tuesday, April 27th, 2010

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 a few records from a larger sequence file - for example, ...

Interleaving paired FASTQ files with Biopython

Monday, December 14th, 2009

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).

Working with FASTQ files in Biopython when speed matters

Friday, September 25th, 2009

Biopython 1.51 onward includes support for Sanger, Solexa and Illumina 1.3+ FASTQ files in Bio.SeqIO, which allows a lot of neat tricks very concisely. For example, the tutorial (PDF) has examples finding and removing primer or adaptor sequences. However, because the Bio.SeqIO interface revolves around SeqRecord objects there is often a ...

Simpler, optimized format conversion with Biopython

Tuesday, September 22nd, 2009

As per Peter's recent post we are using this space to show of a couple of the new features in Biopython 1.52 before it is released. In this post we'll look at the new convert() function that both Bio.SeqIO and Bio.AlignIO will get in Biopython 1.52. No one has ever complained ...

Indexing sequence files with Biopython

Monday, September 21st, 2009

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. This will of course be covered in the Biopython Tutorial & Cookbook (PDF) once this code is released. Suppose you have a large sequence ...

Clever tricks with NCBI Entrez EInfo (& Biopython)

Sunday, June 21st, 2009

Constructing complicated NCBI Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help. For example, suppose you want to search for mitochondrial genomes from a given taxa - either just in the Entrez web interface, for use in a script with ...

Introducing (and expanding) the Biopython Cookbook

Wednesday, April 29th, 2009

Hi all, You may have noticed we're trying out using the wiki for Biopython cookbook entries. It's a new idea so at the moment there are only a few 'recipes' on offer. If you have some tricks you find yourself using time and again to solve a problem why not ...

HOWTO automate tree drawing

Friday, June 15th, 2007

I updated the Trees HowTo with some code demonstrating how to automatically generate postscript trees from newick or nexus tree files. This uses the Bio::Tree::Draw::Cladogram module that will draw Phylograms or Cladograms. With a few unix tools (eps2png and epstopdf [part of TeX]) you can generate png and pdf ...