[Suggestion] New parameters for seqkit rename

[apcamargo]

Right now, seqkit rename doesn't provide users with parameters to tune how the renaming is performed. I recently had to rename duplicated headers using | as a field separator and needed to use awk for that.

Some suggestions:

• Allow custom separators (instead of just _).
• Allow the counter to start from an arbitrary integer (eg. 0).
• Allow to add a suffix to all the headers, regardless if they have duplicates or not.

Those are just suggestions, so feel free to ignore them if you don't think they fit SeqKit's design.

[shenwei356]

Allow custom separators (instead of just _)

Sure, it's easy.

Allow the counter to start from an arbitrary integer (eg. 0).

OK

Allow to add a suffix to all the headers, regardless if they have duplicates or not.

seqkit replace -p '$' -r '_suffix'

[shenwei356]

Added.

• seqkit_darwin_amd64.tar.gz
• seqkit_darwin_arm64.tar.gz
• seqkit_linux_amd64.tar.gz

There are only IDs.

$ echo -ne ">s\na\n>s\nc\n"
>s
a
>s
c

$ echo -ne ">s\na\n>s\nc\n" \
    | seqkit rename  -s '|' -N 0  \
    | seqkit replace -p '$' -r _suffix
>s_suffix
a
>s|0_suffix
c

There are IDs and descriptions.

$ echo -ne ">s a\na\n>s b\nc\n"
>s a
a
>s b
c

$ echo -ne ">s a\na\n>s b\nc\n" \
    | seqkit rename  -s '|' -N 0 \
    | seqkit seq -i \
    | seqkit replace -p '$' -r _suffix
>s_suffix
a
>s|0_suffix
c

[apcamargo]

Thank you! That was really quick!

Allow to add a suffix to all the headers, regardless if they have duplicates or not.

By that I meant the suffix with the counter. So, in your example, it would be something like this:

>s|0
a
>s|1
c

[shenwei356]

I see, we can add another flag to add a count to the first record.

[shenwei356]

Three flags added:

  -1, --rename-1st-rec      rename the first record as well
  -s, --separator string    separator between original ID/name and the counter (default "_")
  -N, --start-num int       starting count number for *duplicated* IDs/names, should be greater than zero (default 2)

• seqkit_darwin_amd64.tar.gz
• seqkit_darwin_arm64.tar.gz
• seqkit_linux_amd64.tar.gz

$ echo -ne ">s a\na\n>s b\nc\n>s2\ng\n"
>s a
a
>s b
c
>s2
g

# default
$ echo -ne ">s a\na\n>s b\nc\n>s2\ng\n"    \
    | seqkit rename  
>s a
a
>s_2 b
c
>s2
g

$ echo -ne ">s a\na\n>s b\nc\n>s2\ng\n"   \
    | seqkit rename  -s '|' -N 1 -1
>s|0 a
a
>s|1 b
c
>s2|0
g

[apcamargo]

Thanks!!