Beginner at Python- My task is to convert a FASTA file to a PHYLIP file (tab-delimited file) and cannot figure out how to do so

Question

[oki4]

My code so far:

temp_line = ''
out_lines = []
with open('dna.fasta.py', 'r') as f_in:
    text = f_in.read()
    text = text.split()
    print(text)
    for line in text:
        line = line.strip('\n')
        if line[0] == '>':
            temp_line = line.strip('>')
            out_lines.append(temp_line)
        else:
            out_lines.append(line)


print (out_lines)
print (temp_line)
with open('dna.phylip.py', 'w') as file_out:
    file_out.write('\n'.join(out_lines))

My Input file: dna.fasta.py

>Human
AGCATGCATCGATCGATCGACTAGCTAGCG
>Chimp
GATATGTCGAGATCGTCAGCTCGATCAGCT
>Gorilla
TGTGTCGATCTCGAGCTGAGTCGTCTATCA

My output file so far: dna.phylip file

Human
AGCATGCATCGATCGATCGACTAGCTAGCG
Chimp
GATATGTCGAGATCGTCAGCTCGATCAGCT
Gorilla
TGTGTCGATCTCGAGCTGAGTCGTCTATCA

Correct Format of the output phylip file/ What it should look like:

Human     AGCATGCATCGATCGATCGACTAGCTAGCG
Chimp     GATATGTCGAGATCGTCAGCTCGATCAGCT
Gorilla     TGTGTCGATCTCGAGCTGAGTCGTCTATCA

I have no idea how to remove the '/n' and add '/t', I've tried the strip and split function (to remove the new line), to add the tab, I've tried joining '/t' but my methods haven't worked. I don't what I'm doing wrong.

Answer 1

[GouthamAtla]

From your program, it looks like you have not properly understood the fasta format.

It could be

>1:id bla bla | bla
ATTATTGTTG
ATTATTGT
ATGGAT
ATTAGGGAGGGGATTA

>2:id bla bla | bla
AGGATTGCGGCTAGG

If you are not hesitant to use BioPython:

import sys
from Bio import SeqIO

for record in SeqIO.parse(sys.argv[1],"fasta"):
        print strrecord.id) + "\t" + record.seq

The text = text.split() does not work with fasta. You need to look for line starts with ">" and then the following lines should be concatenated until you see another line that starts with ">". You can search for how to handle fasta with python in google or in this site.

Answer 2

[Brian Bushnell]

You can do this with the BBMap package like this:

reformat.sh in=file.fasta out=file.oneline

Answer 3

[lakhujanivijay]

If the task matters more than the code/language, here is a perl one liner:

perl -ne 'if($_=~s/^>//){chomp($_), print $_} else{print "\t".$_}' file.fa > out.fa

file.fa

>Human
AGCATGCATCGATCGATCGACTAGCTAGCG
>Chimp
GATATGTCGAGATCGTCAGCTCGATCAGCT
>Gorilla
TGTGTCGATCTCGAGCTGAGTCGTCTATCA

out.fa

Human     AGCATGCATCGATCGATCGACTAGCTAGCG
Chimp     GATATGTCGAGATCGTCAGCTCGATCAGCT
Gorilla     TGTGTCGATCTCGAGCTGAGTCGTCTATCA

PS: Though, I love Python

[GouthamAtla]

It does not work for multi lined fasta files also does not work if there are different words in fasta header like the one below:

>1:id bla bla | bla
ATTATTGTTG
ATTATTGT
ATGGAT
ATTAGGGAGGGGATTA

>2:id bla bla | bla
AGGATTGCGGCTAGG

[lakhujanivijay]

Hi Goutham,

Thanks for pointing that out :)

Fixed the problems, here is the new one liner:

perl -ne 'if($_=~s/^>//){chomp($_), print "\n".$_." "} else{chomp($_),print $_}' file.fa

I hope it is helpful for the person who posted the question.

Answer 4

[Zaag]

with open('dna.fasta.py', 'r') as f, open('dna.phylip.py', 'w') as file_out:
    for line in f:
        line = line.strip()
        print(line)
        if line[0] == '>':
             file_out.write('{}\t'.format(line.strip('>')))
        else:
             file_out.write('{}\n'.format(line))

[oki4]

Thank you! Why do you have to include the {} (brackets) when writing into the output file?

[Zaag]

https://docs.python.org/3/library/string.html

You could just print the variable with a tab or newline.