/get_N_loci

Subsample N loci to reduce an original (big) fasta file

Primary LanguagePython

get_N_loci

You are sad during your PhD?
Fasta files are too big for you?
I HAVE the solution: get_N_loci.py !

how to launch it:

Like that little rabbit:

python3 /home/croux/Programmes/get_N_loci/get_N_loci.py longiflora_grandiflora.fasta 2000

But please, use the V2 version !

BREAKING NEWS: the second version V2 is now AVAILABLE, and THIS, is a REVOLUTION!

Modifications:

  1. now, two filters are applied to the input file (fasta format):
  • threshold: proportion of missing data. If a locus has a proportion of missing data greater than the threshold, then, the locus is rejected.
  • minLoci: if an individual has a number of retained loci smaller than minLoci, then reject the individual.
  1. write some files containing informations.

Output files:

  1. individuals.txt: list of individuals with number of available loci.
  2. retained_loci.txt: informations after filtering.
  3. XXX_filtered_subsampled.fasta: the new filtered and subsampled fasta file.

Example:

Usage:

python3 /home/croux/Programmes/get_N_loci/get_N_loci_v2.py [input file, in a fasta format] [number of loci to sample] [maximum of tolerated missing data per sequence (between 0 and 1)] [minimum number of retained loci (passing the previous threshold). If an individual has less available loci that this number, then the individual is rejected]

Example:

python3 /home/croux/Programmes/get_N_loci/get_N_loci_v2.py longiflora_grandiflora.fasta 5000 0.5 2000