How to sort fasta file numerically
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6 weeks ago

Hi,

I was wondering if there was a way to sort a fasta file so that the chromosomes are in numeric order. Currently, the fasta file is computationally sorted where the chromosomes are order like this

>chr1
>chr10
>chr11
....
>chr2
>chr20

I was wondering if there was a way to sort the fasta file so the chromosomes are sorted numerically like this

>chr1
>chr2
>chr3
...
>chr10
>chr11
Assembly genome sequence • 122 views
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$ seqkit sort -nN test.fa -o test_out.fa
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3
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6 weeks ago
ATpoint 48k

Try:

bioawk -c fastx '{print}' in.fa | sort -k1,1V | awk '{print ">"$1;print $2}'

or any of:

Sort Multiple Fasta Numerically

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I saw that post. I tried Frédéric Mahé post and it doesn't appear to work. I can't seem to get Ih3 answer to work either

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I edited my answer, please try again.

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I believe it is because the orginal post has a different chromosome structure i.e ">chr2_1000-1020"

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Yes, to make Frédéric Mahé answer work with your data, you need to change the -t field of the sort function so that it fits your fasta headers.

sort -t "r" -k2n for instance instead of sort -t "_" -k2n

sed -e '/>/s/^/@/' -e '/>/s/$/#/' file.fasta | tr -d "\n" | tr "@" "\n" | sort -t "r" -k2n | tr "#" "\n" | sed -e '/^$/d'
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That works as well. Thank you!!

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Ahhh I see. Yeah, that works now. Thank you

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