running BLAST (bl2seq) without creating sequence files

Question

I have a script that performs BLAST queries (bl2seq)

The script works like this:

1. Get sequence a, sequence b
2. write sequence a to filea
3. write sequence b to fileb
4. run command 'bl2seq -i filea -j fileb -n blastn'
5. get output from STDOUT, parse
6. repeat 20 million times

The program bl2seq does not support piping. Is there any way to do this and avoid writing/reading to the harddrive?

I'm using Python BTW.

Answer 1

Depending on what OS you're running on, you may be able to use something like bash's process substitution. I'm not sure how you'd set that up in Python, but you're basically using a named pipe (or named file descriptor). That won't work if bl2seq tries to seek within the files, but it should work if it just reads them sequentially.

Answer 2

How do you know bl2seq does not support piping.? By the way, pipes is an OS feature, not the program. If your bl2seq program outputs something, whether to STDOUT or to a file, you should be able to parse the output. Check the help file of bl2seq for options to output to file as well, eg -o option. Then you can parse the file.

Also, since you are using Python, an alternative you can use is BioPython module.