When you have a list of input files that you want to analyze, but the software you are using doesn't support paralelization, a convenient way of speeding up the analysis is by running the program on a subsets of your files at the same time.
If you have a list of input files in one file (input.files.txt), it can easily be split into multiple files using the linux split command.
split -a 2 -l 500 -d input.files.txt input.file.
which will produce files named:
input.file.00
input.file.01
...
input.file.99
with each file containing 500 rows.
Can you use this for fasta files and make sure that fasta id and the sequence don't end up on different files ?
ReplyDeleteI have no idea how to do it.
ReplyDeletehere are other ideas on how to do this for fasta files:
ReplyDeletehttp://biostar.stackexchange.com/questions/1853/code-golf-digesting-fasta-sequences-into-a-set-of-smaller-sequences
thanks frenkiboy for sending the link !! : )
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