Question

Alphabetizing fasta sequence

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7.5 years ago

stacy734 ▴ 40

Hi everyone,

Can someone suggest a method to sort a fasta file by alphabetical order of the sequence (not the defline)?

Any advice will be appreciated.

fasta • 3.4k views

ADD COMMENT • link updated 19 months ago by Ram 44k • written 7.5 years ago by stacy734 ▴ 40

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Do you have a multi-line or single line fasta?

ADD REPLY • link 7.5 years ago by st.ph.n ★ 2.7k

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Thank you all!

Stacy

ADD REPLY • link 7.5 years ago by stacy734 ▴ 40

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it it answer your question, please choose a green mark on the left to close this thead.

ADD REPLY • link 7.5 years ago by Pierre Lindenbaum 164k

score 3 · Answer 1 · 2017-06-14

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7.5 years ago

Brian Bushnell 20k

Using the BBMap package:

shuffle.sh in=file.fasta out=sorted.fasta sequence

ADD COMMENT • link 7.5 years ago by Brian Bushnell 20k

score 2 · Answer 2 · 2017-06-14

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7.5 years ago

Pierre Lindenbaum 164k

linearize and sort...

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}'  roxan.fasta |LC_ALL=C sort -t $'\t' -k2,2 | tr "\t" "\n"

ADD COMMENT • link 7.5 years ago by Pierre Lindenbaum 164k

score 2 · Answer 3 · 2017-06-14

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7.5 years ago

cpad0112 21k

seqkit sort --quiet -s -i <fasta file>

i is ignore case s is sort by sequence

ADD COMMENT • link 7.5 years ago by cpad0112 21k