def raxml(
logfile,
fastafile,
bootstrap=False,
threads=2,
name_conversion=None,
phylipize=False,
verbalise=lambda *a: None,
):
if phylipize:
alignment = internal.make_phylip(fastafile, logfile)
else:
alignment = fastafile
print "phylip done"
if bootstrap:
raxml_best = raxml_phylogeny(alignment,
logfile,
bootstrap=False,
threads=threads)
raxml_bstrap = raxml_phylogeny(alignment,
logfile,
bootstrap=bootstrap,
threads=threads)
raxml_final = apply_boostrap(raxml_best, raxml_bstrap, logfile)
verbalise(
"Y", "Best tree with bootstrap support can be found at %s" %
raxml_final)
else:
print "Starting raxml"
raxml_final = raxml_phylogeny(alignment,
logfile,
bootstrap=bootstrap,
threads=threads)
verbalise("Y", "Best tree can be found at %s" % raxml_final)
if name_conversion:
handle = open(name_conversion, 'rb')
conv_dic = {
line.split()[0]: (line.split()[2], line.split()[1])
for line in handle
}
handle.close()
internal.rename_newick(raxml_final, conversiondic=conv_dic)
return raxml_final
def raxml(logfile, fastafile, bootstrap=False, threads=2,
name_conversion=None, phylipize=False,
verbalise=lambda *a: None, ):
if phylipize:
alignment = internal.make_phylip(fastafile, logfile)
else:
alignment = fastafile
print "phylip done"
if bootstrap:
raxml_best = raxml_phylogeny(alignment,
logfile,
bootstrap=False,
threads=threads)
raxml_bstrap = raxml_phylogeny(alignment,
logfile,
bootstrap=bootstrap,
threads=threads)
raxml_final = apply_boostrap(raxml_best, raxml_bstrap, logfile)
verbalise("Y",
"Best tree with bootstrap support can be found at %s" % raxml_final)
else:
print "Starting raxml"
raxml_final = raxml_phylogeny(alignment,
logfile,
bootstrap=bootstrap,
threads=threads)
verbalise("Y", "Best tree can be found at %s" % raxml_final)
if name_conversion:
handle = open(name_conversion, 'rb')
conv_dic = { line.split()[0]:(line.split()[2], line.split()[1]) for line in handle }
handle.close()
internal.rename_newick(raxml_final, conversiondic=conv_dic)
return raxml_final
mafft_alignment = logfile[:-3] + 'mafft.fa'
external.mafft_align(homolog_fasta, mafft_alignment)
internal.display_alignment(mafft_alignment,
conversiondic=conv_dic,
outfile=logfile[:-3] + 'mafft.png',
showplot=args.display_on,
gapthresh=args.gapthresh)
######### RaXML phylogenetic analysis of alignment #########
"""
Using PROT-LG-GAMMA model, a single tree and no bootstrapping (though all of these
could be setup to allow overriding for fringe case analyses).
"""
verbalise("B", "Running RAxML analysis to construct phylogeny")
final_tree = external.raxml(logfile,
mafft_alignment,
bootstrap=args.bootstrap,
threads=args.threads,
name_conversion=None,
verbalise=verbalise)
raxml_renamed = internal.rename_newick(final_tree, conversiondic=conv_dic)
# clean up temp files and directory
for file in [
homolog_fasta,
]:
if os.path.exists(file):
os.remove(file)
os.rmdir(temp_dir) # dir must be empty!
internal.display_alignment(
mafft_alignment,
conversiondic=conv_dic,
outfile=logfile[:-3] + "mafft.png",
showplot=args.display_on,
gapthresh=args.gapthresh,
)
######### RaXML phylogenetic analysis of alignment #########
"""
Using PROT-LG-GAMMA model, a single tree and no bootstrapping (though all of these
could be setup to allow overriding for fringe case analyses).
"""
verbalise("B", "Running RAxML analysis to construct phylogeny")
final_tree = external.raxml(
logfile,
mafft_alignment,
bootstrap=args.bootstrap,
threads=args.threads,
name_conversion=None,
verbalise=verbalise,
)
raxml_renamed = internal.rename_newick(final_tree, conversiondic=conv_dic)
# clean up temp files and directory
for file in [homolog_fasta]:
if os.path.exists(file):
os.remove(file)
os.rmdir(temp_dir) # dir must be empty!