Question: How do I remove file extension on my genome name in gff3 file?
0
gravatar for eennadi
7 weeks ago by
eennadi0
eennadi0 wrote:

Hello, Please how do I remove _pilon_pilon_pilon from the contig name in my .gff file

contig_844_pilon_pilon_pilon    .   contig  1   137831  .   .   .   ID=contig_844_pilon_pilon_pilon;Name=contig_844_pilon_pilon_pilon
contig_844_pilon_pilon_pilon    maker   gene    68149   78543   .   +   .   ID=CR513_019411;Name=CR513_019411;Alias=maker-contig_844_pilon_pilon_pilon-augustus-gene-0.19;Note=Similar to CR513_49975: Amine oxidase (Fragment) (Mucuna pruriens OX%3D157652);
contig_844_pilon_pilon_pilon    maker   mRNA    68149   78543   .   +   .   ID=CR513_019411-RA;Parent=CR513_019411;Name=CR513_019411-RA;Alias=maker-contig_844_pilon_pilon_pilon-augustus-gene-0.19-mRNA-1;_AED=0.04;_QI=0|0.75|0.6|1|0.5|0.6|5|118|684;_eAED=0.04;Note=Similar to CR513_49975: Amine oxidase (Fragment) (Mucuna pruriens OX%3D157652);
contig_844_pilon_pilon_pilon    maker   exon    68149   68984   .   +   .   ID=CR513_019411-RA:1;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   exon    73517   73898   .   +   .   ID=CR513_019411-RA:2;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   exon    74669   74782   .   +   .   ID=CR513_019411-RA:3;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   exon    76743   77251   .   +   .   ID=CR513_019411-RA:4;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   exon    78212   78543   .   +   .   ID=CR513_019411-RA:5;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   CDS 68149   68984   .   +   0   ID=CR513_019411-RA:cds;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   CDS 73517   73898   .   +   1   ID=CR513_019411-RA:cds;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   CDS 74669   74782   .   +   0   ID=CR513_019411-RA:cds;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   CDS 76743   77251   .   +   0   ID=CR513_019411-RA:cds;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   CDS 78212   78425   .   +   1   ID=CR513_019411-RA:cds;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    maker   three_prime_UTR 78426   78543   .   +   .   ID=CR513_019411-RA:three_prime_utr;Parent=CR513_019411-RA;
contig_844_pilon_pilon_pilon    snap_masked match   2284    4761    7.338   -   .   ID=contig_844_pilon_pilon_pilon:hit:1303782:4.5.0.0;Name=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.16-mRNA-1;target_len
assembly • 108 views
ADD COMMENTlink modified 7 weeks ago by Pierre Lindenbaum131k • written 7 weeks ago by eennadi0
0
gravatar for JC
7 weeks ago by
JC11k
Mexico
JC11k wrote:

sed "s/_pilon_pilon_pilon//g" < input.gff > output.gff

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by JC11k
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