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;