split all fasta sequences in a multi fasta file from half into two sequences

Question

[manishbiotechie]

Hi i have a fasta file with many fasta sequences and I want to split all the fasta sequences into two half from middle.. I am new to bioinformatics kindly suggest some tool or perl command

[lakhujanivijay]

You should first either use the biostars search utility to look for similar post or you can google like this to get answers from biostars.org.

on google.com : split fasta site:www.biostars.org

So, we recommend you to first look for similar post, try one of the answers mentioned by other users,and then post the issues that you may face adding specific details of the commands use.

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[manishbiotechie]

I know how to split a big fasta files into multiple fasta files but my query is to bisect all fasta nucleotide sequences in a fasta file into two halves e.g.

>TC93917
GGCACGAGGCAGAAACCAATTTCAAAACATTATATAAATAGCTAGTTTCAGTACTAGCTG
TGCAACTCAATTATAGAACAATGGCTTCCTCTATGATCTCCTCTTCAGCTATCACTACAG
TTAACCGTGCCTCTCCGGTACAATCCGGTGCGGTGGCTCCATTCGTCGGACTCAAGTCCA
TGGCTGGCTTCCCAATTACAAAGGTCAACAAAGACATTACCTCCATTACAAGCAATGGTG
GAAGAGTAAACTGCATGCAGGTGTGGCCTCCTATTGGCAAGAAGAAGTTTGAGACTCTTT
CATATCTTCCACCATTGACCAGAGAACAATTGGCGAAAGAAGTTGAATACCTTATAAGGA
AGGGATGGGTTGCTTGCTTGGAATTCGAGACCGAGAAAGGATTTGTGTACCGTGAGAACC
ACAGTTCACCAGGATACTATGACGGACGTTACTGGACAATGTGGAAGTTGCCTTTGTTTG
GAGCAACTGATGCTTCTCAAGTGTTGAAGGAGCTTGATGAAGTTGTTGCTGCTTACCCTA
CTGCCTTTGTCCGTATCATCGGATTCGACAATGTTCGTCAAGTTCAATGCATCAGTTTCA
TTGCACACACACCTGATGTTTACTAAGTTCATTGCACTGGAATTTGGAAGAACTTTTTTC
TTCTTCCCATTTATGTTTTGCTTTTAATTTCCATTTCTTTTTCAGGGAAATGTTTTCCTT
CTGTGTTTTTATATTTCTGTTTTTGGATTTGAAAAATGGGATGTATAAGATTAAGAGTTA
ATGAATGAAATGGTTACTTAATTCCCAAAGTACTTAAAAGAATCCATTATCTATGTAGTT
TTCCTTGTTCTGC

into

>TC93917_1
GGCACGAGGCAGAAACCAATTTCAAAACATTATATAAATAGCTAGTTTCAGTACTAGCTG
TGCAACTCAATTATAGAACAATGGCTTCCTCTATGATCTCCTCTTCAGCTATCACTACAG
TTAACCGTGCCTCTCCGGTACAATCCGGTGCGGTGGCTCCATTCGTCGGACTCAAGTCCA
TGGCTGGCTTCCCAATTACAAAGGTCAACAAAGACATTACCTCCATTACAAGCAATGGTG
GAAGAGTAAACTGCATGCAGGTGTGGCCTCCTATTGGCAAGAAGAAGTTTGAGACTCTTT
CATATCTTCCACCATTGACCAGAGAACAATTGGCGAAAGAAGTTGAATACCTTATAAGGA
AGGGATGGGTTGCTTGCTTGGAATTCGAGACCGAGAAAGGATTTGTGTACCGTGAGAACC
ACAGTTC

>TC93917_2
ACCAGGATACTATGACGGACGTTACTGGACAATGTGGAAGTTGCCTTTGTTTG
GAGCAACTGATGCTTCTCAAGTGTTGAAGGAGCTTGATGAAGTTGTTGCTGCTTACCCTA
CTGCCTTTGTCCGTATCATCGGATTCGACAATGTTCGTCAAGTTCAATGCATCAGTTTCA
TTGCACACACACCTGATGTTTACTAAGTTCATTGCACTGGAATTTGGAAGAACTTTTTTC
TTCTTCCCATTTATGTTTTGCTTTTAATTTCCATTTCTTTTTCAGGGAAATGTTTTCCTT
CTGTGTTTTTATATTTCTGTTTTTGGATTTGAAAAATGGGATGTATAAGATTAAGAGTTA
ATGAATGAAATGGTTACTTAATTCCCAAAGTACTTAAAAGAATCCATTATCTATGTAGTT
TTCCTTGTTCTGC

sorry if i asked this simple thing but as i told i am new to bioinfo

[lakhujanivijay]

Hello manishbiotechie,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

I know how to split a big fasta files into multiple fasta files

You should explain this by adding your code here. May be people can suggest how you can edit / expand your code.

[Kevin Blighe]

Why do you need to [literally] split the sequence in half? It should be possible to do with awk.

Answer 1

[5heikki]

Assuming no linebreaks in sequences:

awk '{if(/^>/){H1=$0"_1";H2=$0"_2"}else{print H1"\n"substr($0,1,length($0)/2)"\n"H2"\n"substr($0,length($0)/2+1)}}' seq.fa