physcripts/infer_tree_from_fasta.py at master · chinchliff/physcripts · GitHub

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#!/usr/bin/env python

if __name__ == '__main__':

    import os, sys

    if len(sys.argv) < 2:
        print "infer_tree_from_fasta.py <fastafile> [--noalign] [--noclean]"
        sys.exit(0)

    fastafile = sys.argv[1]
    alnname = fastafile.rsplit(".fasta",1)[0]

    doalign = True
    docleannames = True
    if len(sys.argv) > 2:
        for arg in sys.argv[2:]:
            if arg == "--noalign":
            doalign = False
            elif arg == "--nocleannames":
                docleannames = False

    if docleannames:
        cleanerargs = ["clean_gb_names_simple_fasta.py", fastafile]
        os.system(" ".join(cleanerargs))
        cleanedfasta = fastafile.rsplit(".fasta",1)[0] + ".cleaned.fasta"
        fastatoalign = cleanedfasta
    else:
        fastatoalign = fastafile

    if doalign:
        alignedfasta = fastatoalign + ".aligned"
        mafftargs = ["mafft", fastatoalign, ">", alignedfasta]
        os.system(" ".join(mafftargs))
        fastatoconvert = alignedfasta
    else:
        fastatoconvert = fastatoalign

    phylipfile = alnname + ".phy"
    fasta2phylipargs = ["fasta2phylip", fastatoconvert, phylipfile]

    os.system(" ".join(fasta2phylipargs))

    raxmlargs = ["raxmlHPC-PTHREADS-SSE3", \
                    "-s", phylipfile, \
                    "-n", alnname, \
                    "-p", "123", \
                    "-m", "GTRCAT", \
                    "-T", "4"]

    os.system(" ".join(raxmlargs))

    figtreeargs = ["figtree", "RAxML_bestTree." + alnname]
    os.system(" ".join(figtreeargs))