Run the code with the help -h flag and it will pull down some options.
python PolyFastA.py -h
It will output something like this:
usage: PolyFastA.py [-h] [--file FILE] [--dir DIR] [--pops [pop1,pop2,pop3]] [--out OUT] [--pipe] [--cds] [--silent] [--name NAME] [--jc]
Fast estimator of nucleotide diversity (theta_pi),
Watterson's theta (theta_w), and Tajimas's D for coding and
non-coding sequences
optional arguments:
-h, --help show this help message and exit
--file FILE, -f FILE an alignment in FASTA format.
--dir DIR, -d DIR directory containing FASTA files only.
--pops [pop1,pop2,pop3], -p [pop1,pop2,pop3]
split alignment by populations. A comma-separated list of strings that are found in the sequence headers.
--out OUT, -o OUT name of output file. (default/empty will print to screen
--pipe, -i if FASTA file is being piped in from STDIN.
--cds, -c the alignment is protein coding. Will split into synonymous and nonsynonymous sites.
--silent, -s suppress header and verbose output.
--name NAME, -n NAME name of the DNA region to show in output.
--jc Jukes-Cantor correction for Pi.
It can also print a vector of the folded site frequency spectrum and
correct theta_pi for multiple hits (jukes-cantor).
Examples:
python PolyFastA.py -f myAlignment.fas -p pop1,pop2
"-p pop1,pop2" assumes that the alignment has sequences that are labeled:
>pop1_ind1_XXX
ATGC...
>pop1_ind2_XXX
ATGC...
>pop2_ind1_XXX
ATGC...
>pop2_ind2_XXX
Alignment is inframe cooding sequence:
python PolyFastA.py -f myAlignment.fas -p pop1,pop2 --cds
Want Jukes-Cantor corrected estimates for CDS:
python PolyFastA.py -f myAlignment.fas -p pop1,pop2 --cds --jc
FASTA files in directory:
python PolyFastA.py -d myFastaDir/ --out allpoly.csv
Read from pipe:
python PolyFastA.py --pipe -p pop1,pop2
The format is not strict but the identifier (e.g. pop1) needs to be somewhere in the header.