[Samtools-devel] blast2sam.pl script

[timothee c. <tc...@st...>]

Hi Folks,

I had a few issues using blast2sam.pl script provided with samtools so I 
modified it and I thought I could share the modified script.
Here are the changes that I made.
 * Print the query sequence in sam format and add a dummy quality string 
of A (21)
 * Correct a small bug where deletion and insertion were swapped
 * Handle multiple hits for one query in several sam lines
 * Handle the new blast+ format along with the old blast format

Any comment is welcome.
btw does anybody know if there would be a sensible way of transforming 
blast e value in a phred like mapping quality?

Thanks

Tim
----------------------------------------------------------------------------------------------

Exemple of how I use the script:
* Old format
blast-2.2.22/bin/megablast -d reference.fasta -i query.fasta | 
samtools-0.1.7_x86_64-linux/blast2sam.pl | 
samtools-0.1.7_x86_64-linux/samtools view -bT reference.fasta - | 
samtools-0.1.7_x86_64-linux/samtools sort - query_sorted
 * New format
blast+2.2.22/bin/blastn -task dc-megablast -db reference_genes.fasta 
-query query.fasta | sed 's/lcl|//' | | 
samtools-0.1.7_x86_64-linux/blast2sam.pl | 
samtools-0.1.7_x86_64-linux/samtools view -bT reference.fasta - | 
samtools-0.1.7_x86_64-linux/samtools sort - query_sorted

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.