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I have a gff file in which I need to remove -R* from all lines that have the pattern Parent=gopAga1_........-R.;

The file structure is below shown for a single gene, but I need a global fix for all genes in the file.

>2446 17292 . + . ID=gopAga1_00004497-RA;Parent=gopAga1_00004497;Name=gopAga1_00004497-RA;Alias=augustus_masked-scaffold4362-processed-gene-0.0-mRNA-1;_AED=0.12;_QI=0|0.8|0.81|1|1|1|11|1368|404;_eAED=0.12;Note=Similar to PLAT: Tissue-type plasminogen activator (Pongo abelii);

>scaffold4362 maker exon 2446 2545 . + . ID=gopAga1_00004497-RA:exon:4045;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 6721 6834 . + . ID=gopAga1_00004497-RA:exon:4046;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 7241 7415 . + . ID=gopAga1_00004497-RA:exon:4047;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 10114 10205 . + . ID=gopAga1_00004497-RA:exon:4048;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 10478 10649 . + . ID=gopAga1_00004497-RA:exon:4049;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 11037 11122 . + . ID=gopAga1_00004497-RA:exon:4050;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 11518 11713 . + . ID=gopAga1_00004497-RA:exon:4051;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 12794 12930 . + . ID=gopAga1_00004497-RA:exon:4052;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 13006 13146 . + . ID=gopAga1_00004497-RA:exon:4053;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 14920 15047 . + . ID=gopAga1_00004497-RA:exon:4054;Parent=gopAga1_00004497-RA;

>scaffold4362 maker exon 16051 17292 . + . ID=gopAga1_00004497-RA:exon:4055;Parent=gopAga1_00004497-RA;

I am using sed to find patterns but I am unsure how to use sed to remove everything between the last number of the line and semi-colon.

Will my current script work? The expected output is below.

sed 's/Parent=gopAga1_........-R.;$/Parent=gopAga1........;/ gop.gff

>2446 17292 . + . ID=gopAga1_00004497-RA;Parent=gopAga1_00004497;Name=gopAga1_00004497-RA;Alias=augustus_masked-scaffold4362-processed-gene-0.0-mRNA-1;_AED=0.12;_QI=0|0.8|0.81|1|1|1|11|1368|404;_eAED=0.12;Note=Similar to PLAT: Tissue-type plasminogen activator (Pongo abelii);

>scaffold4362 maker exon 2446 2545 . + . ID=gopAga1_00004497-RA:exon:4045;Parent=gopAga1_00004497;

>scaffold4362 maker exon 6721 6834 . + . ID=gopAga1_00004497-RA:exon:4046;Parent=gopAga1_00004497;

>scaffold4362 maker exon 7241 7415 . + . ID=gopAga1_00004497-RA:exon:4047;Parent=gopAga1_00004497;

>scaffold4362 maker exon 10114 10205 . + . ID=gopAga1_00004497-RA:exon:4048;Parent=gopAga1_00004497;

>scaffold4362 maker exon 10478 10649 . + . ID=gopAga1_00004497-RA:exon:4049;Parent=gopAga1_00004497;

>scaffold4362 maker exon 11037 11122 . + . ID=gopAga1_00004497-RA:exon:4050;Parent=gopAga1_00004497;

>scaffold4362 maker exon 11518 11713 . + . ID=gopAga1_00004497-RA:exon:4051;Parent=gopAga1_00004497;

>scaffold4362 maker exon 12794 12930 . + . ID=gopAga1_00004497-RA:exon:4052;Parent=gopAga1_00004497;

>scaffold4362 maker exon 13006 13146 . + . ID=gopAga1_00004497-RA:exon:4053;Parent=gopAga1_00004497;

>scaffold4362 maker exon 14920 15047 . + . ID=gopAga1_00004497-RA:exon:4054;Parent=gopAga1_00004497;

>scaffold4362 maker exon 16051 17292 . + . ID=gopAga1_00004497-RA:exon:4055;Parent=gopAga1_00004497;

Maybe:

sed 's/-R[^;]*;$/;/'

Or

awk -F ';' -f OFS=';' 'sub(/-R.*/, "",$(NF-1)); 1'

$ sed '/^>.*Parent=samp1_/s/-R.;$/;/' <file.fa
>ID=samp1_00004497:4045;Parent=samp1_00004497;
>ID=samp1_00004497:4046;Parent=samp1_00004498;
>ID=samp1_00004497:4047;Parent=samp1_00004499;
>ID=samp1_00004497:4048;Parent=samp1_00004496;

The sed command above will find all lines starting with > and containing the string Parent=samp1_, and for each such line replace the final -R.; (where the . matches a single character) with just ;. Lines not ending with anything matching -R.; would remain unaltered.

Change the dot in -R.; to [^;]* if you want to remove any number of non-; character up to the ; at the end.

For your updated question, use Parent=gopAga1_ in place of Parent=samp1_.

The commandline

sed -re 's/([^-]+).+?;/1;/g'

will output everything up to - for each line, not including - and then append a semicolon to the end.

Update

sed -re 's/(_.8)-R./1/g'

will remove unwanted characters based on presence of _ then 8 chars then -R.