[Biopython-dev] BWA Wrapper

[Saket Choudhary]

Hi,

I am writing a bwa wrapper for bio-python. I have infact got the "index"
 option working. However I have a concern:

bwa has these options :



bwa index -a bwtsw database.fasta

bwa aln database.fasta short_read.fastq > aln_sa.sai

bwa samse database.fasta aln_sa.sai short_read.fastq > aln.sam

bwa sampe database.fasta aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln.sam

bwa bwasw database.fasta long_read.fastq > aln.sam


If you read the documentation here<http://bio-bwa.sourceforge.net/bwa.shtml>,
you will see that  "-r" is an option with "aln" command as well as the
"samse" command. In the former it is of type INT and in the latter of type
STR. Now I am not sure how can this be taken care of in the wrapper,
because I also plan to implement a checker_function.  One way is to make a
new class, lets say BwaAlignCommand which will take care of all options
inside the "aln" command and separately implement another class say
"BwaSamseCommand", and implement all the options of the "samse" command.
But I am not sure if that is indeed the correct way of addressing the
problem.


Any pointers on this issue ?



Thanks


Saket Choudhary

Undergraduate Student

IIT Bombay,India