import os
from sys import argv
from subprocess import Popen, PIPE
from Bio.SeqIO import convert

print("WARNING! This script only uses default settings.")

#conversion
inp = str(input("Provide file name: "))
inp_form = str.lower( input("Provide file format: "))
out = str(input("Provide output name: "))
out_form = str.lower(input("Provide desired output's format: "))

convert(inp, inp_form, out, out_form)

print("Procedure done. File", out, "was created.")

#distance matrix creator
print("Creation of the distance matrix started.")
suppressed = open(os.devnull, 'w')
protdist = Popen(['phylip', 'protdist'], stdin = PIPE, stdout = suppressed)
inp = input(str("Enter input name: "))
protdist.communicate((inp + "\ny\n").encode())
out = input(str("Enter output name: "))
os.rename('outfile', out)
print(out, "file was created")

#Neighbor joining method
print("Neighbor joining method program")
nj = Popen(['phylip', 'neighbor'], stdin = PIPE, stdout = suppressed)
inp_nj = input(str("Enter input name: "))
nj.communicate((inp_nj + "\ny\n").encode())
out_nj_f = input(str("Provide name for outfile: "))
out_nj_t = input(str("Provide name for tree file: "))
os.rename('outfile', out_nj_f)
os.rename('outtree', out_nj_t)
print(out_nj_f, out_nj_t, "files were created.")

#Maximum Parsimony method
print("Maximum parsimony program")
mp = Popen(['phylip', 'protpars'], stdin = PIPE, stdout = suppressed)
inp_mp = input(str("Enter input name: "))
mp.communicate((inp_mp + "\ny\n").encode())
out_mp_f = input(str("Enter name for outfile: "))
out_mp_t = input(str("Enter name for tree file: "))
os.rename("outfile", out_mp_f)
os.rename("outtree", out_mp_t)
print(out_mp_f, out_mp_t, "files were created.")

#Maximum Likelyhood method
print("Maximum likelyhood program")
ml = Popen(['phylip', 'proml'], stdin = PIPE, stdout = suppressed)
inp_ml = input(str("Enter input name: "))
ml.communicate((inp_mp + "\ny\n").encode())
out_ml_f = input(str("Enter name for outfile: "))
out_ml_t = input(str("Enter name for tree file: "))
os.rename("outfile", out_ml_f)
os.rename("outtree", out_ml_t)
print(out_mp_f, out_mp_t, "files were created.")

print("All files were created. Procedure done.")
suppressed.close()

376be146a83125d573cfd8f1d197db1d8861ef77
<mask token>

<mask token>
print('WARNING! This script only uses default settings.')
<mask token>
convert(inp, inp_form, out, out_form)
print('Procedure done. File', out, 'was created.')
print('Creation of the distance matrix started.')
<mask token>
protdist.communicate((inp + '\ny\n').encode())
<mask token>
os.rename('outfile', out)
print(out, 'file was created')
print('Neighbor joining method program')
<mask token>
nj.communicate((inp_nj + '\ny\n').encode())
<mask token>
os.rename('outfile', out_nj_f)
os.rename('outtree', out_nj_t)
print(out_nj_f, out_nj_t, 'files were created.')
print('Maximum parsimony program')
<mask token>
mp.communicate((inp_mp + '\ny\n').encode())
<mask token>
os.rename('outfile', out_mp_f)
os.rename('outtree', out_mp_t)
print(out_mp_f, out_mp_t, 'files were created.')
print('Maximum likelyhood program')
<mask token>
ml.communicate((inp_mp + '\ny\n').encode())
<mask token>
os.rename('outfile', out_ml_f)
os.rename('outtree', out_ml_t)
print(out_mp_f, out_mp_t, 'files were created.')
print('All files were created. Procedure done.')
suppressed.close()

<mask token>
print('WARNING! This script only uses default settings.')
inp = str(input('Provide file name: '))
inp_form = str.lower(input('Provide file format: '))
out = str(input('Provide output name: '))
out_form = str.lower(input("Provide desired output's format: "))
convert(inp, inp_form, out, out_form)
print('Procedure done. File', out, 'was created.')
print('Creation of the distance matrix started.')
suppressed = open(os.devnull, 'w')
protdist = Popen(['phylip', 'protdist'], stdin=PIPE, stdout=suppressed)
inp = input(str('Enter input name: '))
protdist.communicate((inp + '\ny\n').encode())
out = input(str('Enter output name: '))
os.rename('outfile', out)
print(out, 'file was created')
print('Neighbor joining method program')
nj = Popen(['phylip', 'neighbor'], stdin=PIPE, stdout=suppressed)
inp_nj = input(str('Enter input name: '))
nj.communicate((inp_nj + '\ny\n').encode())
out_nj_f = input(str('Provide name for outfile: '))
out_nj_t = input(str('Provide name for tree file: '))
os.rename('outfile', out_nj_f)
os.rename('outtree', out_nj_t)
print(out_nj_f, out_nj_t, 'files were created.')
print('Maximum parsimony program')
mp = Popen(['phylip', 'protpars'], stdin=PIPE, stdout=suppressed)
inp_mp = input(str('Enter input name: '))
mp.communicate((inp_mp + '\ny\n').encode())
out_mp_f = input(str('Enter name for outfile: '))
out_mp_t = input(str('Enter name for tree file: '))
os.rename('outfile', out_mp_f)
os.rename('outtree', out_mp_t)
print(out_mp_f, out_mp_t, 'files were created.')
print('Maximum likelyhood program')
ml = Popen(['phylip', 'proml'], stdin=PIPE, stdout=suppressed)
inp_ml = input(str('Enter input name: '))
ml.communicate((inp_mp + '\ny\n').encode())
out_ml_f = input(str('Enter name for outfile: '))
out_ml_t = input(str('Enter name for tree file: '))
os.rename('outfile', out_ml_f)
os.rename('outtree', out_ml_t)
print(out_mp_f, out_mp_t, 'files were created.')
print('All files were created. Procedure done.')
suppressed.close()

import os
from sys import argv
from subprocess import Popen, PIPE
from Bio.SeqIO import convert
print('WARNING! This script only uses default settings.')
inp = str(input('Provide file name: '))
inp_form = str.lower(input('Provide file format: '))
out = str(input('Provide output name: '))
out_form = str.lower(input("Provide desired output's format: "))
convert(inp, inp_form, out, out_form)
print('Procedure done. File', out, 'was created.')
print('Creation of the distance matrix started.')
suppressed = open(os.devnull, 'w')
protdist = Popen(['phylip', 'protdist'], stdin=PIPE, stdout=suppressed)
inp = input(str('Enter input name: '))
protdist.communicate((inp + '\ny\n').encode())
out = input(str('Enter output name: '))
os.rename('outfile', out)
print(out, 'file was created')
print('Neighbor joining method program')
nj = Popen(['phylip', 'neighbor'], stdin=PIPE, stdout=suppressed)
inp_nj = input(str('Enter input name: '))
nj.communicate((inp_nj + '\ny\n').encode())
out_nj_f = input(str('Provide name for outfile: '))
out_nj_t = input(str('Provide name for tree file: '))
os.rename('outfile', out_nj_f)
os.rename('outtree', out_nj_t)
print(out_nj_f, out_nj_t, 'files were created.')
print('Maximum parsimony program')
mp = Popen(['phylip', 'protpars'], stdin=PIPE, stdout=suppressed)
inp_mp = input(str('Enter input name: '))
mp.communicate((inp_mp + '\ny\n').encode())
out_mp_f = input(str('Enter name for outfile: '))
out_mp_t = input(str('Enter name for tree file: '))
os.rename('outfile', out_mp_f)
os.rename('outtree', out_mp_t)
print(out_mp_f, out_mp_t, 'files were created.')
print('Maximum likelyhood program')
ml = Popen(['phylip', 'proml'], stdin=PIPE, stdout=suppressed)
inp_ml = input(str('Enter input name: '))
ml.communicate((inp_mp + '\ny\n').encode())
out_ml_f = input(str('Enter name for outfile: '))
out_ml_t = input(str('Enter name for tree file: '))
os.rename('outfile', out_ml_f)
os.rename('outtree', out_ml_t)
print(out_mp_f, out_mp_t, 'files were created.')
print('All files were created. Procedure done.')
suppressed.close()

import os
from sys import argv
from subprocess import Popen, PIPE
from Bio.SeqIO import convert

print("WARNING! This script only uses default settings.")

#conversion
inp = str(input("Provide file name: "))
inp_form = str.lower( input("Provide file format: "))
out = str(input("Provide output name: "))
out_form = str.lower(input("Provide desired output's format: "))

convert(inp, inp_form, out, out_form)

print("Procedure done. File", out, "was created.")

#distance matrix creator
print("Creation of the distance matrix started.")
suppressed = open(os.devnull, 'w')
protdist = Popen(['phylip', 'protdist'], stdin = PIPE, stdout = suppressed)
inp = input(str("Enter input name: "))
protdist.communicate((inp + "\ny\n").encode())
out = input(str("Enter output name: "))
os.rename('outfile', out)
print(out, "file was created")

#Neighbor joining method
print("Neighbor joining method program")
nj = Popen(['phylip', 'neighbor'], stdin = PIPE, stdout = suppressed)
inp_nj = input(str("Enter input name: "))
nj.communicate((inp_nj + "\ny\n").encode())
out_nj_f = input(str("Provide name for outfile: "))
out_nj_t = input(str("Provide name for tree file: "))
os.rename('outfile', out_nj_f)
os.rename('outtree', out_nj_t)
print(out_nj_f, out_nj_t, "files were created.")

#Maximum Parsimony method
print("Maximum parsimony program")
mp = Popen(['phylip', 'protpars'], stdin = PIPE, stdout = suppressed)
inp_mp = input(str("Enter input name: "))
mp.communicate((inp_mp + "\ny\n").encode())
out_mp_f = input(str("Enter name for outfile: "))
out_mp_t = input(str("Enter name for tree file: "))
os.rename("outfile", out_mp_f)
os.rename("outtree", out_mp_t)
print(out_mp_f, out_mp_t, "files were created.")

#Maximum Likelyhood method
print("Maximum likelyhood program")
ml = Popen(['phylip', 'proml'], stdin = PIPE, stdout = suppressed)
inp_ml = input(str("Enter input name: "))
ml.communicate((inp_mp + "\ny\n").encode())
out_ml_f = input(str("Enter name for outfile: "))
out_ml_t = input(str("Enter name for tree file: "))
os.rename("outfile", out_ml_f)
os.rename("outtree", out_ml_t)
print(out_mp_f, out_mp_t, "files were created.")

print("All files were created. Procedure done.")
suppressed.close()
