to grep pattern

Question

[sherafzalk769]

I am interested to grep the line only containing the word "gene" present at column 3 of this following file but this word is also present at each line in column 9 of this file. Please any suggestion to use the grep in bash/linux and select only the line which has word "gene" at column 3 of this file. thanks..

HiC_scaffold_5  maker   gene    42689882        42692012        .       +       .       ID "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11"; Name "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11"; 0
HiC_scaffold_5  maker   mRNA    42689882        42692012        .       +       .       ID "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1"; Name "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1"; Parent "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11"; _AED "0.36"; _QI "0|0|0|0.5|1|1|2|0|160"; _eAED "1.00";        0
HiC_scaffold_5  maker   exon    42689882        42690273        .       +       .       ID "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1:1"; Parent "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1";
       0
HiC_scaffold_5  maker   exon    42691922        42692012        .       +       .       ID "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1:2"; Parent "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1";
       0
HiC_scaffold_5  maker   CDS     42689882        42690273        .       +       0       ID "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1:cds"; Parent "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1";
     0
HiC_scaffold_5  maker   CDS     42691922        42692012        .       +       1       ID "IDmodified-cds-15717"; Parent "augustus_masked-@000000F|arrow|arrow-processed-gene-0.11-mRNA-1";    0
HiC_scaffold_5  maker   gene    42938430        42944293        .       +       .       ID "maker-@000000F|arrow|arrow-snap-gene-4.61"; Name "maker-@000000F|arrow|arrow-snap-gene-4.61";       0
HiC_scaffold_5  maker   mRNA    42938430        42944293        .       +       .       ID "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1"; Name "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1"; Parent "maker-@000000F|arrow|arrow-snap-gene-4.61"; _AED "0.34"; _QI "0|0|0|0.66|0|0.33|3|0|256"; _eAED "0.83"; 0
HiC_scaffold_5  maker   exon    42938430        42938991        .       +       .       ID "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1:1"; Parent "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1";     0
HiC_scaffold_5  maker   exon    42939695        42939894        .       +       .       ID "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1:2"; Parent "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1";     0
HiC_scaffold_5  maker   exon    42944285        42944293        .       +       .       ID "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1:3"; Parent "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1";     0
HiC_scaffold_5  maker   CDS     42938430        42938991        .       +       0       ID "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1:cds"; Parent "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1";   0
HiC_scaffold_5  maker   CDS     42939695        42939894        .       +       2       ID "IDmodified-cds-21469"; Parent "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1";   0
HiC_scaffold_5  maker   CDS     42944285        42944293        .       +       0       ID "IDmodified-cds-21470"; Parent "maker-@000000F|arrow|arrow-snap-gene-4.61-mRNA-1";   0

Answer 1

[dariober]

I would use awk instead so you can be explicit about selecting column 3:

awk -v FS='\t' -v OFS='\t' '$3 == "gene"' in.gff

With grep I would probably do:

grep -P '\tgene\t' in.gff