How to concatenate sequences in the same multiFASTA files and then print result to a new FASTA file?-CodePudding

I have a folder with over 50 FASTA files each with anywhere from 2-8 FASTA sequences within them, here's an example:


    testFOR.id_AH004930.fasta

>AH004930|2:1-128_Miopithecus_talapoin
ATGA
>AH004930|2:237-401_Miopithecus_talapoin
GGGT
>AH004930|2:502-580_Miopithecus_talapoin
CTTTGCT
>AH004930|2:681-747_Miopithecus_talapoin
GGTG

    testFOR.id_M95099.fasta

>M95099|1:1-90_Homo_sapien
TCTTTGC
>M95099|1:100-243_Homo_sapien
ATGGTCTTTGAA

They're all grouped based on their ID number (in this case AH004930 and M95099), which I've managed to extract from the original raw multiFASTA file using the very handy seqkit code found HERE.

What I am aiming to do is:

Use cat to put these sequences together within the file like this:

>AH004930|2:1-128_Miopithecus_talapoin
ATGAGGGTCTTTGCTGGTG

>M95099|1:1-90_Homo_sapien
TCTTTGCATGGTCTTTGAA

(I'm not fussed about the nucleotide position, I'm fussed about the ID and species name!)

Print this result out into a new FASTA file.

Ideally I'd really like to have all of these 50 files condensed into 1 FASTA that I can then go ahead and filter/align:


    GENE_L.fasta

>AH004930|2:1-128_Miopithecus_talapoin
ATGAGGGTCTTTGCTGGTG
>M95099|1:1-90_Homo_sapien
TCTTTGCATGGTCTTTGAA
....

So far I have found a way to achieve what I want but only one file at a time (using this code: cat myfile.fasta | sed -e '1!{/^>.*/d;}' | sed ':a;N;$!ba;s/\n//2g' > output.fasta which I've sadly lost the link for the credit for) but a lot of these file names are very similar, so it's inevitable that if I did it manually, I'd miss some/it would be way too slow.

I have tried to put this into a loop and it's kind of there! But what it does is it cats each FASTA file, put's it into a new one BUT only keeps the first header, leaving me with a massive stitched together sequence;

for FILE in *; do cat *.fasta| sed -e '1!{/^>.*/d;}'| sed ':a;N;$!ba;s/\n//2g' > output.fasta; done
 

    output.fasta

>AH004930|2:1-128_Miopithecus_talapoin
ATGAGGGTCTTTGCTGGTGTCTTTGCATGGTCTTTGAAGGTCTTTGAAATGAGTGGT...

I wondered if making a loop similar to the one HERE would be any good but I am really unsure how to get it to print each header once it opens a new file.

How can I cat these sequences, print them into a new file and still keep these headers? I would really appreciate any advice on where I've gone wrong in the loop and any solutions suitable for a zsh shell! I'm open to any python or linux solution. Thank you kindly in advance

CodePudding user response：

Not sure I understand exactly your issue, but if you simply want to concatenate contents from many files to a single file I believe the (Python) code below should work:

import os

input_folder = 'path/to/your/folder/with/fasta/files'
output_file = 'output.fasta'

with open(output_file, 'w') as outfile:
    for file_name in os.listdir(input_folder):
        if not file_name.endswith('.fasta'):  # ignore this
            continue
        file_path = os.path.join(input_folder, file_name)
        with open(file_path, 'r') as inpfile:
            outfile.write(inpfile.read())

CodePudding user response：

This might work for you (GNU sed):

sed -s '1h;/>/d;H;$!d;x;s/\n//2g' file1 file2 file3 ...

Set -s to treat each file separately.

Copy the first line.

Delete any other lines containing >.

Append all other lines to the first.

Delete these lines except for the last.

At the end of the file, swap to the copies and remove all newlines except the first.

Repeat for all files.