Do fast bowtie with option -c

[OrsonMM]

Hello

I tried to use these command like a subrutine in my python script
seq1 = CATGTAGCTAG
subprocess.call(bowtie -c index.bwt seq1)

But it takes around 3s. for each search, And I have a lot of seqs. And I need do fast. Exist a possible do more efficient in my code.

Pd: I now that if I use a file that contain all my seqs, bowtie is fast and efficient.

Saludos.

[BenLangmead]

I think you're stuck putting all your queries in a file and running them all at once, as you suggest. I understand that might not fit your use case. The way you're running bowtie repeatedly, you're unavoidably causing the executable to start up repeatedly and load the index repeatedly and those things take a lot of time compared to aligning a single read.