Question: Splitting Multifasta file to individual files
0
gravatar for merzanaeem007
5 weeks ago by
merzanaeem0070 wrote:

Hello, I'm a molecular biology undergraduate interested in bioinformatics. I started this project where I need as much HIV1 I could, I downloaded the whole seq available in HIV.lanl however they come as a huge single multifasta file and I need each seq in a seperate file for my analysis. downloading each seq 1 by 1 would take forever (given its 12K), I tried the EMBOSS split tool but uploading 400MB files crashes every time at around the 10%. I searched for some manual ways but with my little to none programming skill (yet) I could figure it out on my own. I came across this python script https://github.com/ramsainanduri/split_multi_fasta but its a script and despite playing with it for a few days I couldn't figure out how to edit it such that it takes my HIV1db.fasta as input and split it (I'm a windows user and installed python and know how to open the script in shell).. I have checked the similar posts on the forum too but none breaks it down to no-low programming educated one. If someone could take the time and effort to explain it as to a retard I would totally appreciate it, especially the part how i set the path of the input part :(

ADD COMMENTlink modified 5 weeks ago by wljlinksly50 • written 5 weeks ago by merzanaeem0070

I find it hard to believe that you did not find a suitable answer here on the forum.

some examples:

in general search for "split multifasta file" , "convert multi to single fasta file" ....

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by lieven.sterck8.5k
3
gravatar for Juke34
5 weeks ago by
Juke344.6k
Sweden
Juke344.6k wrote:

Have a look at here : Tutorial: FASTA file split

ADD COMMENTlink written 5 weeks ago by Juke344.6k

Thanks alot, the SEDA tool was perfect for my work, appreciate it alot :)

ADD REPLYlink written 5 weeks ago by merzanaeem0070
2
gravatar for wljlinksly
5 weeks ago by
wljlinksly50
wljlinksly50 wrote:

you can download this repo: https://github.com/wulj2/fa2fas

and execute make command in the repo,

you will get the desired fa2fas executable binary

./fa2fas

 Usage: fa2fs [options]

 Options: -i FILE input fasta file

          -o DIR output directory
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by wljlinksly50
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