Entering edit mode
2.6 years ago
sherafzalk769
▴
10
grep -w -f upregulated_genes_in_BEg GCA_900659725.1_ASM90065972v1_genomic.gff
LOCUS10095
LOCUS10108
LOCUS10129
LOCUS10130
LOCUS10152
LOCUS10161
LOCUS10225
LOCUS10252
LOCUS10266
LOCUS10268
LOCUS10294
LOCUS10313
LOCUS10351
LOCUS10355
LOCUS10358
Gff file:
CAACVG010000011.1 EMBL exon 112774 112954 . + . ID=exon-CALMAC_LOCUS4-2-3;Parent=rna-CALMAC_LOCUS4-2;Note=source:maker%3B~ID:CALMACT00000015207;gbkey=mRNA;locus_tag=CALMAC_LOCUS4;product=DNA-directed RNA polymerase II 16 kDa polypeptide;standard_name=rpb4tada2a_iso3
CAACVG010000011.1 EMBL exon 121098 121359 . + . ID=exon-CALMAC_LOCUS4-2-4;Parent=rna-CALMAC_LOCUS4-2;Note=source:maker%3B~ID:CALMACT00000015207;gbkey=mRNA;locus_tag=CALMAC_LOCUS4;product=DNA-directed RNA polymerase II 16 kDa polypeptide;standard_name=rpb4tada2a_iso3
CAACVG010000011.1 EMBL CDS 83091 83151 . + 0 ID=cds-VEN33461.1;Parent=rna-CALMAC_LOCUS4-2;Dbxref=NCBI_GP:VEN33461.1;Name=VEN33461.1;Note=source:maker%3B~ID:CALMACC00000015207;gbkey=CDS;locus_tag=CALMAC_LOCUS4;product=VEN33461.1;protein_id=VEN33461.1
CAACVG010000011.1 EMBL CDS 112774 112954 . + 2 ID=cds-VEN33461.1;Parent=rna-CALMAC_LOCUS4-2;Dbxref=NCBI_GP:VEN33461.1;Name=VEN33461.1;Note=source:maker%3B~ID:CALMACC00000015207;gbkey=CDS;locus_tag=CALMAC_LOCUS4;product=VEN33461.1;protein_id=VEN33461.1
CAACVG010000011.1 EMBL CDS 121098 121272 . + 1 ID=cds-VEN33461.1;Parent=rna-CALMAC_LOCUS4-2;Dbxref=NCBI_GP:VEN33461.1;Name=VEN33461.1;Note=source:maker%3B~ID:CALMACC00000015207;gbkey=CDS;locus_tag=CALMAC_LOCUS4;product=VEN33461.1;protein_id=VEN33461.1
CAACVG010000011.1 EMBL mRNA 82779 101822 . + . ID=rna-CALMAC_LOCUS4-3;Parent=gene-CALMAC_LOCUS4;Note=source:maker%3B~ID:CALMACT00000015206;gbkey=mRNA;locus_tag=CA
Did not work because your search string (pattern) does not seem to be present in example posted above?
I think LOCUS* is present in the gff file. Do you think it is not enough or not a complete pattern?
Entries in the file contain the word
CALMAC
before_LOCUS
. So you will need to adjust your search patterns or not use-w
option.