Question

Write a Python program that converts an input file in FASTA format, called "fasta.txt", to an output file in PHYLIP format called "phylip.txt". For example, if the input file contains: >human ACCGTTATAC CGATCTCGCA >chimp ACGGTTATAC CGTACGATCG >monkey ACCTCTATAC CGATCGATCC >gorilla ATCTATATAC CGATCGATCG Then the output file should be human ACCGTTATACCGATCTCGCA chimp ACGGTTATACCGTACGATCG monkey ACCTCTATACCGATCGATCC gorilla ATCTATATACCGATCGATCG

FASTA format has a description (indicated with a '>') followed by 1 or more lines of a DNA sequence. PHYLIP format has a description followed by a single line of a DNA sequence and each sequence is the same length. For this homework, the input file will have an arbitrary number of sequences of arbitrary, but identical, length.

Answer 1

def Manage(str):

ls=list(str)

ls.remove('>')

position=0

for i in range(0,len(ls)):

if ls[i]==' ':

position=i

break

newlist=[]

for i in range(position,len(ls)):

if ls[i]!=' ':

newlist.append(ls[i])

str=""

for i in range(0,position):

str=str+ls[i]

str=str+" "

for i in newlist:

str=str+i

file = open('phylip.txt','a')

file.write(str)

file.close()

file=open("fasta.txt",'r')

for each in file:

Manage(each)# reading each line from file

file.close()

# we created simple list to remove space

# iterate to remove all spaces

#conver list into string