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InputForAsral.py
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#!/usr/bin/env python
# coding: utf-8
#on ubuntu
# In[1]:
#family of 8
from Bio import SeqIO
import dendropy
from dendropy.interop import raxml
for j in range(1,11):
globals()["bb"+ str(j)]=dendropy.TreeList()
##for j in range(1,7):
## globals()["taxa8n"+ str(j)]=[]
##for j in range(1,7):
## globals()["bp8nont"+ str(j)]=[]
for j in range(1,7):
output="/mnt/e/sugerc/family of 8 alignment/f8y"+ str(j)+"-aligned.fasta"
globals()["data8y"+ str(j)]=dendropy.DnaCharacterMatrix.get(path=output, schema="fasta")
rx = raxml.RaxmlRunner()
globals()["tree8y"+ str(j)] = rx.estimate_tree(char_matrix= globals()["data8y"+ str(j)], raxml_args=["--no-bfgs"])
#globals()["tree8ybp"+ str(j)]=dendropy.Tree.encode_bipartitions(globals()["tree8y"+ str(j)])
#for i in range(len(globals()["tree8ybp"+ str(j)])):
# if(globals()["tree8ybp"+ str(j)][i].is_trivial()== False):
# globals()["bp8nont"+ str(j)].append(globals()["tree8ybp"+ str(j)][i])
cc=0
with open(output) as read_file:
records = SeqIO.parse(output, 'fasta')
for record in records:
v = record.description
##globals()["taxa8n"+ str(j)].append(v[len(v)-1])
cc=v[len(v)-3:len(v)-1]
if(cc != "10"):
cc=cc[len(cc)-1] # cc homeology set 1-10 # change globals()["tree8y"+ str(j)] taxon names one by one
for w in range(globals()["tree8y"+ str(j)].taxon_namespace.__len__()):
#print(w)
globals()["tree8y"+ str(j)].taxon_namespace[w].label=globals()["tree8y"+ str(j)].taxon_namespace[w].__str__()[len(globals()["tree8y"+ str(j)].taxon_namespace[w].__str__())-2:len(globals()["tree8y"+ str(j)].taxon_namespace[w].__str__())-1]
globals()["bb"+ str(cc)].append(globals()["tree8y"+ str(j)]) # make b TreeList #bk homeology set b1-b10
# In[2]:
#family of 7
from Bio import SeqIO
import dendropy
from dendropy.interop import raxml
#for j in range(1,48):
# globals()["taxa7n"+ str(j)]=[]
#for j in range(1,48):
# globals()["bp7nont"+ str(j)]=[]
for j in range(1,48):
output="/mnt/e/sugerc/family of 7 alignment/f7y"+ str(j)+"-aligned.fasta"
globals()["data7y"+ str(j)]=dendropy.DnaCharacterMatrix.get(path=output, schema="fasta")
rx = raxml.RaxmlRunner()
globals()["tree7y"+ str(j)] = rx.estimate_tree(char_matrix= globals()["data7y"+ str(j)], raxml_args=["--no-bfgs"])
#globals()["tree7ybp"+ str(j)]=dendropy.Tree.encode_bipartitions(globals()["tree7y"+ str(j)])
#for i in range(len(globals()["tree7ybp"+ str(j)])):
# if(globals()["tree7ybp"+ str(j)][i].is_trivial()== False):
# globals()["bp7nont"+ str(j)].append(globals()["tree7ybp"+ str(j)][i])
cc=0
with open(output) as read_file:
records = SeqIO.parse(output, 'fasta')
for record in records:
v = record.description
# globals()["taxa7n"+ str(j)].append(v[len(v)-1])
cc=v[len(v)-3:len(v)-1]
if(cc != "10"):
cc=cc[len(cc)-1]
for w in range(globals()["tree7y"+ str(j)].taxon_namespace.__len__()):
#print(w)
globals()["tree7y"+ str(j)].taxon_namespace[w].label=globals()["tree7y"+ str(j)].taxon_namespace[w].__str__()[len(globals()["tree7y"+ str(j)].taxon_namespace[w].__str__())-2:len(globals()["tree7y"+ str(j)].taxon_namespace[w].__str__())-1]
globals()["bb"+ str(cc)].append(globals()["tree7y"+ str(j)]) # make b TreeList #bk homeology set b1-b10
# In[3]:
#family of 6
from Bio import SeqIO
import dendropy
from dendropy.interop import raxml
#for j in range(1,234):
# globals()["taxa6n"+ str(j)]=[]
#for j in range(1,234):
# globals()["bp6nont"+ str(j)]=[]
for j in range(1,234):
output="/mnt/e/sugerc/family of 6 alignment/f6y"+ str(j)+"-aligned.fasta"
globals()["data6y"+ str(j)]=dendropy.DnaCharacterMatrix.get(path=output, schema="fasta")
rx = raxml.RaxmlRunner()
globals()["tree6y"+ str(j)] = rx.estimate_tree(char_matrix= globals()["data6y"+ str(j)], raxml_args=["--no-bfgs"])
#globals()["tree6ybp"+ str(j)]=dendropy.Tree.encode_bipartitions(globals()["tree6y"+ str(j)])
#for i in range(len(globals()["tree6ybp"+ str(j)])):
# if(globals()["tree6ybp"+ str(j)][i].is_trivial()== False):
# globals()["bp6nont"+ str(j)].append(globals()["tree6ybp"+ str(j)][i])
cc=0
with open(output) as read_file:
records = SeqIO.parse(output, 'fasta')
for record in records:
v = record.description
#globals()["taxa6n"+ str(j)].append(v[len(v)-1])
cc=v[len(v)-3:len(v)-1]
if(cc != "10"):
cc=cc[len(cc)-1]
for w in range(globals()["tree6y"+ str(j)].taxon_namespace.__len__()):
#print(w)
globals()["tree6y"+ str(j)].taxon_namespace[w].label=globals()["tree6y"+ str(j)].taxon_namespace[w].__str__()[len(globals()["tree6y"+ str(j)].taxon_namespace[w].__str__())-2:len(globals()["tree6y"+ str(j)].taxon_namespace[w].__str__())-1]
globals()["bb"+ str(cc)].append(globals()["tree6y"+ str(j)])
# In[10]:
# input ready
for a in range(1,11):
pat="/mnt/c/Users/Asus/Desktop/astral/Astral/Mine-sugarcane/homeologySet"+str(a)+".tre"
globals()["bb"+str(a)].write(path=pat,schema="newick")
# In[14]:
# outputs of cmd call astral
import dendropy as dn
for i in range(1,11):
t=dn.Tree.get(path="/mnt/c/Users/Asus/Desktop/astral/Astral/Mine-sugarcane/outputs/OutputHomeologySet"+str(i)+".tre",schema="newick")
t.print_plot()
print(t.as_string(schema="newick"))
# In[15]:
import dendropy as dn
for i in range(1,11):
t=dn.Tree.get(path="/mnt/c/Users/Asus/Desktop/astral/Astral/Mine-sugarcane/outputs/OutputHomeologySet"+str(i)+".tre",schema="newick")
#t.print_plot()
print(t.as_string(schema="newick"))