convert csv to fasta format using python

Question

[Abdellrhmanakl]

i have a tsv file and i want to convert it to fasta please help

Moderator edit note: I have removed the link as it provided a direct link to an archive download and could present a risk.

Example data should be provided as a text snippet

[liorglic]

Please include a short sample from your input and desired output.

[jv]

https://biopython.org/wiki/SeqIO

[bngan]

SeqIO.convert doesn't work with TSV's. I would recommend removing the tabs via iteration then joining the lists together in a new fasta file.

Hope this helps.

[jv]

SeqIO can read and write tab-delimited sequence files and it is my understanding that a TSV file is a tab-delimited file so I'm not sure what the issue would be

Answer 1

[Sareh]

CSV file INPUT:

seq_name1,ACTACTACT
seq_name2,CGTCGTCGTCGT

FASTA file OUTPUT:

> seq_name1
ACTACTACT
> seq_name2
CGTCGTCGTCGT

METHOD with no packages

# OPEN IN & OUT files
in_handle = open(in_path, "r")
out_handle = open(out_path, "w")

# read in the file
for line in in_handle:
    line_tuple = line.strip("\n").split(',')  # for TSV just change this to split('\t')
    header = line_tuple[0] # column 1
    seq = line_tuple[1] # column 2

    # WRITE out the edited TSV
    out_handle.write("> {}\n{}\n".format(header, seq))

in_handle.close()
out_handle.close()

Be aware of any spaces before or after the comma in a CSV and within the seq name if you want to remove them.

[Ram]

I'd recommend adding the rtrim/ltrim once you get the header and seq and also not adding the space after the > in the output. Otherwise, excellent solution!