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I need to rename the following headers from a FASTA file. Something like:

>ENST00000488147.1::chr1:29570-30013(-)
>ENST00000405392.5::chr2:24919186-24920186(-)

into different format like this:

>chr1:29570-30013(-)_ENST00000488147.1
>chr2:24919186-24920186(-)_ENST00000405392.5

How can I rename the FASTA headers, perhaps using sed or awk?

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    $\begingroup$ Is there fasta sequence between the headers? If so is it multiline or single line fasta? Also what about Biopython? $\endgroup$
    – M__ ♦
    May 24, 2020 at 20:16
  • $\begingroup$ Hi Michael. Yes, there are fasta sequences between the headers, and it has a large number of fasta sequences alongside their headers for each. I didn't know anything about Biopython, but I just looked it up and it seems really helpful as it has motif analysis tools (MEME or MAST). Thank you $\endgroup$
    – taeju
    May 25, 2020 at 12:42

4 Answers 4

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awk -F "::" '{if($1~">"){gsub(">","");print ">"$2"_"$1} else {print $0}}' foo.fa

Basically the same as from Devon but using -F to indicate the initial field delimiter and then using gsub to remove the >.

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  • $\begingroup$ Hello ATpoint. Thank you for your answer. I should've used gsub instead of sed to remove the string that I don't want. Thank you for your answer $\endgroup$
    – taeju
    May 25, 2020 at 12:51
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awk 'BEGIN{FS="::"}{if($1~">"){printf(">%s_%s\n",$2,substr($1,2))}else{print $0}}' input_file.fa > output.fa

An explanation of the non-obvious bits:

  • BEGIN{FS="::"} split columns using :: as the designator
  • $1~">" If there's a > in the line
  • substr($1,2) Trim the > that was at the beginning of the line.
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  • $\begingroup$ awk -F:: '{sub(/>/, ">" $2 "_"); print}' KDM4A_1kbp_TSS.fasta > KDM4A_1kbp_TSS_swp.fasta sed 's/::chr.*)//' KDM4A_1kbp_TSS_swp.fasta > KDM4A_1kbp_TSS_MEMEinput.fasta I just checked your answer now. I had tried working by myself and come up with this script. But, yours looks much better than mine :) I appreciate it for your answer. $\endgroup$
    – taeju
    May 25, 2020 at 12:49
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sed -E 's/>(.+)::(.+)/>\2_\1/' in.fa > out.fa

If you want to use sed.

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    $\begingroup$ This misses the > at the beginning of each name: sed -r 's/>(.+)::(.+)/>\2_\1/' for linux and sed -E 's/>(.+)::(.+)/>\2_\1/' for macOS. $\endgroup$
    – user3051
    May 25, 2020 at 12:55
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    $\begingroup$ Sorry there was a little typo. Now it should work properly $\endgroup$
    – Mr_Z
    May 25, 2020 at 13:00
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I would use perl here instead of sed so you can use non-greedy patterns (e.g. .*?) and so ensure that you always match the first occurrence of :: if there are more than one on the line. Perl also has -i, and in fact is where sed got the idea from, so you can edit the file in place just like you can with sed.

Using this example file:

$ cat file.fa
>ENST00000488147.1::chr1:29570-30013(-)
ACCTCTGAGAGCACCTCTGAGAGCACCTCTGAGAGCACCTCTGAGAGC
ATATATCGGCATATATCGGCATATATCGGCATATATCGGCATATATCG
>ENST00000405392.5::chr2:24919186-24920186(-)
ACTCTAGGATATCGCGATATCGCCTTAGGCTAGAATCGGCTTAGC
TCGCGATATCATCGCCTTAGGCTAGAATCGTCTAGGATATCGCG
CCTTAGGCTATCATCGCCTAGAATCGTCTAGGATATCGAATC

You can do:

$ perl -pe 's/>(.+?)::(.*)/>$2_$1/' file.fa 
>chr1:29570-30013(-)_ENST00000488147.1
ACCTCTGAGAGCACCTCTGAGAGCACCTCTGAGAGCACCTCTGAGAGC
ATATATCGGCATATATCGGCATATATCGGCATATATCGGCATATATCG
>chr2:24919186-24920186(-)_ENST00000405392.5
ACTCTAGGATATCGCGATATCGCCTTAGGCTAGAATCGGCTTAGC
TCGCGATATCATCGCCTTAGGCTAGAATCGTCTAGGATATCGCG
CCTTAGGCTATCATCGCCTAGAATCGTCTAGGATATCGAATC

Or, to edit the file in place:

$ perl -i -pe 's/>(.+?)::(.*)/>$2_$1/' file.fa 
$ cat file.fa
>chr1:29570-30013(-)_ENST00000488147.1
ACCTCTGAGAGCACCTCTGAGAGCACCTCTGAGAGCACCTCTGAGAGC
ATATATCGGCATATATCGGCATATATCGGCATATATCGGCATATATCG
>chr2:24919186-24920186(-)_ENST00000405392.5
ACTCTAGGATATCGCGATATCGCCTTAGGCTAGAATCGGCTTAGC
TCGCGATATCATCGCCTTAGGCTAGAATCGTCTAGGATATCGCG
CCTTAGGCTATCATCGCCTAGAATCGTCTAGGATATCGAATC

Explanation

  • perl -pe: print each line of the input file after applying the script given by -e to it.
  • s/>(.+?)::(.*)/>$2_$1/': the s/old/new/ is the substitution operator and will replace old with new. Here, we look for the shortest stretch of one or more characters (.+?) from the > until the first occurrence of ::, and capture it as $1 (because the pattern is in parentheses). Everything after the first :: is then captured as $2 ((.*)). Then, we replace everything we matched with a >, then the 2nd captured pattern, an underscore and the first captured pattern.

Just for fun, here's a golfed awk approach:

$ awk -F'::' '$0=sub(/>/,"")?">"$2"_"$1:$0' file.fa
>chr1:29570-30013(-)_ENST00000488147.1
ACCTCTGAGAGCACCTCTGAGAGCACCTCTGAGAGCACCTCTGAGAGC
ATATATCGGCATATATCGGCATATATCGGCATATATCGGCATATATCG
>chr2:24919186-24920186(-)_ENST00000405392.5
ACTCTAGGATATCGCGATATCGCCTTAGGCTAGAATCGGCTTAGC
TCGCGATATCATCGCCTTAGGCTAGAATCGTCTAGGATATCGCG
CCTTAGGCTATCATCGCCTAGAATCGTCTAGGATATCGAATC
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