How to sort gff3 according to chromosome order?
Hello, Curious to know on how to sort the gff3 file according to its chromosome while keeping its parent (gene) and child features (mRNA, cds and exon) intact:
input example:
Chr6 EVM gene 212579245 212580018 . + . ID=evm.TU.Chr6.3631;Name=EVM prediction Chr6.3631
Chr6 EVM mRNA 212579245 212580018 . + . ID=evm.model.Chr6.3631;Parent=evm.TU.Chr6.3631;Name=EVM prediction Chr6.3631
Chr6 EVM exon 212579245 212580018 . + . ID=evm.model.Chr6.3631.exon1;Parent=evm.model.Chr6.3631
Chr6 EVM CDS 212579245 212580018 . + 0 ID=cds.evm.model.Chr6.3631;Parent=evm.model.Chr6.3631
Chr5 EVM gene 240103107 240104618 . + . ID=evm.TU.Chr5.3135;Name=EVM prediction Chr5.3135
Chr5 EVM mRNA 240103107 240104618 . + . ID=evm.model.Chr5.3135;Parent=evm.TU.Chr5.3135;Name=EVM prediction Chr5.3135
Chr5 EVM exon 240103107 240104618 . + . ID=evm.model.Chr5.3135.exon1;Parent=evm.model.Chr5.3135
Chr5 EVM CDS 240103107 240104618 . + 0 ID=cds.evm.model.Chr5.3135;Parent=evm.model.Chr5.3135
Chr3 EVM gene 3535391 3537315 . - . ID=evm.TU.Chr3.57;Name=EVM prediction Chr3.57
Chr3 EVM mRNA 3535391 3537315 . - . ID=evm.model.Chr3.57;Parent=evm.TU.Chr3.57;Name=EVM prediction Chr3.57
Chr3 EVM exon 3535391 3535825 . - . ID=evm.model.Chr3.57.exon3;Parent=evm.model.Chr3.57
Chr3 EVM exon 3535934 3536077 . - . ID=evm.model.Chr3.57.exon2;Parent=evm.model.Chr3.57
Chr3 EVM exon 3536230 3537315 . - . ID=evm.model.Chr3.57.exon1;Parent=evm.model.Chr3.57
Chr3 EVM CDS 3535391 3535825 . - 0 ID=cds.evm.model.Chr3.57;Parent=evm.model.Chr3.57
Chr3 EVM CDS 3535934 3536077 . - 0 ID=cds.evm.model.Chr3.57;Parent=evm.model.Chr3.57
Chr3 EVM CDS 3536230 3537315 . - 0 ID=cds.evm.model.Chr3.57;Parent=evm.model.Chr3.57
expected output example:
Chr3 EVM gene 3535391 3537315 . - . ID=evm.TU.Chr3.57;Name=EVM prediction Chr3.57
Chr3 EVM mRNA 3535391 3537315 . - . ID=evm.model.Chr3.57;Parent=evm.TU.Chr3.57;Name=EVM prediction Chr3.57
Chr3 EVM exon 3535391 3535825 . - . ID=evm.model.Chr3.57.exon3;Parent=evm.model.Chr3.57
Chr3 EVM exon 3535934 3536077 . - . ID=evm.model.Chr3.57.exon2;Parent=evm.model.Chr3.57
Chr3 EVM exon 3536230 3537315 . - . ID=evm.model.Chr3.57.exon1;Parent=evm.model.Chr3.57
Chr3 EVM CDS 3535391 3535825 . - 0 ID=cds.evm.model.Chr3.57;Parent=evm.model.Chr3.57
Chr3 EVM CDS 3535934 3536077 . - 0 ID=cds.evm.model.Chr3.57;Parent=evm.model.Chr3.57
Chr3 EVM CDS 3536230 3537315 . - 0 ID=cds.evm.model.Chr3.57;Parent=evm.model.Chr3.57
Chr5 EVM gene 240103107 240104618 . + . ID=evm.TU.Chr5.3135;Name=EVM prediction Chr5.3135
Chr5 EVM mRNA 240103107 240104618 . + . ID=evm.model.Chr5.3135;Parent=evm.TU.Chr5.3135;Name=EVM prediction Chr5.3135
Chr5 EVM exon 240103107 240104618 . + . ID=evm.model.Chr5.3135.exon1;Parent=evm.model.Chr5.3135
Chr5 EVM CDS 240103107 240104618 . + 0 ID=cds.evm.model.Chr5.3135;Parent=evm.model.Chr5.3135
Chr6 EVM gene 212579245 212580018 . + . ID=evm.TU.Chr6.3631;Name=EVM prediction Chr6.3631
Chr6 EVM mRNA 212579245 212580018 . + . ID=evm.model.Chr6.3631;Parent=evm.TU.Chr6.3631;Name=EVM prediction Chr6.3631
Chr6 EVM exon 212579245 212580018 . + . ID=evm.model.Chr6.3631.exon1;Parent=evm.model.Chr6.3631
Chr6 EVM CDS 212579245 212580018 . + 0 ID=cds.evm.model.Chr6.3631;Parent=evm.model.Chr6.3631
Regards, B
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Pierre Lindenbaum
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BioinfoBee •
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uh ? what about the sort command ?
it does sort but not able to keep the child features (mRNA, CDS, exon) in proper order. For example, I can sort using: sort -k1,1 -k4,4n -k5,5n input.gff3 > output_sorted.gff3 but the output would look something like below:
You're sorting by chromosome AND co-ordinates. Try just
sort -k1,1using sort -k1,1 doesn't keep the order of child features of each gene in output.
Those are your options with the
sortutility - you can either keep the existing order or re-order by coordinate. If you're looking for a way to address any possible sorting problems, try gff3sort. You could use--preciseto get to the recommended way entries are supposed to be sorted. If that works, I''ll add this as an answer and you can accept it.