https://github.com/fjruizruano/ngs-protocols
Tip revision: 39a091d1fa569a7fc717ac73c4b3de07f0a1204d authored by fjruizruano on 03 August 2023, 11:48:27 UTC
adding gfa2fas.py and extract_gfa.py
adding gfa2fas.py and extract_gfa.py
Tip revision: 39a091d
massive_phylogenies_figure.py
#!/usr/bin/python
from Bio import Phylo
import matplotlib
#matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab
import sys
print "massive_phylogeny_figure.py NewickList [Outgroup]"
try:
lista = sys.argv[1]
except:
lista = raw_input("Introduce List of Newick files: ")
try:
outgroup = sys.argv[2]
except:
outgroup = raw_input("Introduce outgroup name (optioal):")
newicks = open(lista).readlines()
for newick in newicks:
newick = newick[:-1]
tree = Phylo.read(newick,"newick")
og = ""
# tree.root_with_outgroup({"name": ""})
if outgroup is not "":
for clade in tree.find_clades():
clade = str(clade)
if clade.find(outgroup) != -1:
og = clade
tree.root_with_outgroup({"name": og})
tree.ladderize()
#Phylo.draw_ascii(tree)
Phylo.draw(tree, do_show=False)
pylab.axis("off")
plt.suptitle(newick, fontsize=20)
pylab.savefig(newick+".pdf",format='pdf', bbox_inches='tight', dpi=300)