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In this article Xiaobian for you to introduce in detail the "perl corresponding gff file format is what", detailed content, clear steps, details handled properly, I hope that this "perl corresponding gff file format is what" article can help you solve doubts, the following follow the editor's ideas slowly in-depth, together to learn new knowledge bar.

The corresponding gff file is in the following format:

1 araport11 gene 3631 5899. +. ID=gene:AT1G01010;Name=NAC001;biotype=protein_coding1 araport11 mRNA 3631 5899. +. ID=transcript:AT1G01010.1;Parent=gene:AT1G010101 araport11 five_prime_UTR 3631 3759. +. Parent=transcript:AT1G01010.11 araport11 exon 3631 3913. +. Parent=transcript:AT1G01010.1;Name=AT1G01010.1.exon1;constitutive=11 araport11 CDS 3760 3913. + 0 ID=CDS:AT1G01010.1;Parent=transcript:AT1G01010.1;protein_id=AT1G01010.11 araport11 exon 3996 4276. +. Parent=transcript:AT1G01010.1;Name=AT1G01010.1.exon2;constitutive=11 araport11 CDS 3996 4276. + 2 ID=CDS:AT1G01010.1;Parent=transcript:AT1G01010.1;protein_id=AT1G01010.11 araport11 exon 4486 4605. +. Parent=transcript:AT1G01010.1;Name=AT1G01010.1.exon3;constitutive=11 araport11 gene 6788 9130. -. ID=gene:AT1G01020;Name=ARV1;biotype=protein_coding1 araport11 mRNA 6788 8737. -. ID=transcript:AT1G01020.6;Parent=gene:AT1G01020;biotype=protein_coding1 araport11 exon 6788 7069. -. Parent=transcript:AT1G01020.6;Name=AT1G01020.2.exon8;constitutive=01 araport11 three_prime_UTR 6788 7069. -. Parent=transcript:AT1G01020.61 araport11 three_prime_UTR 7157 7314. -. Parent=transcript:AT1G01020.61 araport11 exon 7157 7450. -. Parent=transcript:AT1G01020.6;Name=AT1G01020.2.exon7;constitutive=01 araport11 CDS 7315 7450. -1 ID=CDS:AT1G01020.6;Parent=transcript:AT1G01020.6;protein_id=AT1G01020.61 araport11 exon 7564 7649. -. Parent=transcript:AT1G01020.6;Name=AT1G01020.1.exon6;constitutive=1

When the script encounters the third column gene of the gff file, it matches gene_id, but different platforms and software gene_id have different prefixes. As shown in the figure above, the prefix is ID=gene:, so when the script matches:

$a [8] = ~ m/ID=gene: ([^;] *); /

If the gene_id in the eighth column of your gff file also has a different prefix, such as the following:

1 araport11 gene 11649 13714. -. ID=AT1G01030;Name=NGA3;biotype=protein_coding

You just need to modify the script to change the match to something like this:

$a [8] = ~ mram ID = ([^;] *); /

So that the script can match correctly and extract the information.

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