Topological sorting of gff features#
It might be critical to have a GFF/GTF file properly sorted:
- Not properly sorted, a genome browser can bug or give wrong displays
- Some tools require files sorted in a particular way (e.g.tabix tool from htslib need a GFF sorted by chromosomes and positions).
- It makes it easy to ready for the human eye
Zhigang Lu has made a nice post about his experience trying to find a way to get a correct topological sorting. See here.
Table of Contents#
Tests summary#
| tool | option in command line | Type of sorting | Comment |
|---|---|---|---|
| AGAT | --tabix | by chromosomes, by gene position, by type (mRNAs then exon, then CDS then alphabetical feature types; then mRNA2 then exon2, then CDS2 then alphabetical feature2 types) | Fix GFF/GTF if needed |
| GenomeTools | -sortlines -tidy -retainids | by chromosomes and positions then random feature type | Lines with the same chromosomes and start positions would be placed randomly, so parent feature lines might sometimes be placed after their children lines. |
| GenomeTools | -retainids | by chromosomes, by gene position, by type (mRNA then children; then mRNA2 then children2), by position (children are sorted by positions) | |
| GFF3sort | --precise | by chromosomes and positions then attribute with Parent attribute first. | move lines with "Parent=" attributes (case insensitive) behind lines without "Parent=" attributes. The goal of GFF3sort is not to obtain a topological sorting but rather getting something that could be indexed optimally by third part tools. |
| gffread | By default, chromosomes are kept in the order they were found. With --sort-alpha parameter the chromosomes (reference sequences) are sorted alphabetically | /!\ Some feature types are lost e.g. gene, three_prime_UTR, five_prime_UTR, etc... |
Example 1#
This test is based on the file used by Zhigang Lu
The GFF file to sort#
##gff-version 3
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS gene 103403 151162 0.12 - . ID=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.02 - . ID=Smp_315690.1;Parent=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.1 - . ID=Smp_315690.2;Parent=Smp_315690
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 103441 103770 0.93 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 103441 103770 0.96 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 105920 106144 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 105920 106144 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 106876 107159 0.93 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 106876 107159 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 140582 140849 0.85 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 140582 140849 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.2
Results#
AGAT#
AGAT v1.0.0
- default sorting
agat_convert_sp_gxf2gxf.pl --gff test.gff
##gff-version 3
SM_V7_1 AUGUSTUS gene 103403 151162 0.12 - . ID=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.02 - . ID=Smp_315690.1;Parent=Smp_315690
SM_V7_1 AUGUSTUS exon 103403 103770 . - . ID=exon-1;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 142981 143205 . - . ID=exon-6;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 145395 145678 . - . ID=exon-8;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 151075 151162 . - . ID=exon-10;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 103441 103770 0.93 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . ID=five_prime_utr-1;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . ID=three_prime_utr-1;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.1 - . ID=Smp_315690.2;Parent=Smp_315690
SM_V7_1 AUGUSTUS exon 103403 103770 . - . ID=exon-2;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 105920 106144 . - . ID=exon-3;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 106876 107159 . - . ID=exon-4;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 140582 140849 . - . ID=exon-5;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 142981 143205 . - . ID=exon-7;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . ID=exon-9;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 151075 151162 . - . ID=exon-11;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 103441 103770 0.96 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 105920 106144 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 106876 107159 0.93 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 140582 140849 0.85 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . ID=five_prime_utr-2;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . ID=three_prime_utr-2;Parent=Smp_315690.2
- Tabix sorting
agat config --expose --tabix agat_convert_sp_gxf2gxf.pl --gff test.gff
##gff-version 3
SM_V7_1 AUGUSTUS gene 103403 151162 0.12 - . ID=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.02 - . ID=Smp_315690.1;Parent=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.1 - . ID=Smp_315690.2;Parent=Smp_315690
SM_V7_1 AUGUSTUS exon 103403 103770 . - . ID=exon-1;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . ID=three_prime_utr-1;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 103403 103770 . - . ID=exon-2;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . ID=three_prime_utr-2;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 103441 103770 0.93 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 103441 103770 0.96 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 105920 106144 . - . ID=exon-3;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 105920 106144 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 106876 107159 . - . ID=exon-4;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 106876 107159 0.93 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 140582 140849 . - . ID=exon-5;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 140582 140849 0.85 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 142981 143205 . - . ID=exon-6;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 142981 143205 . - . ID=exon-7;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . ID=exon-8;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 145395 145678 . - . ID=exon-9;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 151075 151162 . - . ID=exon-10;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 151075 151162 . - . ID=exon-11;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . ID=five_prime_utr-1;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . ID=five_prime_utr-2;Parent=Smp_315690.2
GenomeTools#
GenomeTools 1.6.1
gt gff3 -sortlines -tidy -retainids test.gff
##gff-version 3
##sequence-region SM_V7_1 103403 151162
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS gene 103403 151162 0.12 - . ID=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.02 - . ID=Smp_315690.1;Parent=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.1 - . ID=Smp_315690.2;Parent=Smp_315690
SM_V7_1 AUGUSTUS CDS 103441 103770 0.96 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 103441 103770 0.93 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 105920 106144 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 105920 106144 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 106876 107159 0.93 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 106876 107159 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 140582 140849 0.85 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 140582 140849 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.2
gt gff3 -retainids test.gff
##gff-version 3
##sequence-region SM_V7_1 103403 151162
SM_V7_1 AUGUSTUS gene 103403 151162 0.12 - . ID=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.02 - . ID=Smp_315690.1;Parent=Smp_315690
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 103441 103770 0.93 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.1 - . ID=Smp_315690.2;Parent=Smp_315690
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 103441 103770 0.96 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 105920 106144 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 105920 106144 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 106876 107159 0.93 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 106876 107159 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 140582 140849 0.85 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 140582 140849 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.2
###
GFF3sort#
GFF3sort 0.1.a1a2bc9
gff3sort.pl --precise test.gff
##gff-version 3
SM_V7_1 AUGUSTUS gene 103403 151162 0.12 - . ID=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.02 - . ID=Smp_315690.1;Parent=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.1 - . ID=Smp_315690.2;Parent=Smp_315690
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 103441 103770 0.93 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 103441 103770 0.96 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 105920 106144 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 105920 106144 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 106876 107159 0.93 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 106876 107159 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 140582 140849 0.85 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 140582 140849 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.2
gffread#
gffread v0.11.4
gffread test.gff
# gffread test.gff
# gffread v0.11.4
##gff-version 3
SM_V7_1 AUGUSTUS mRNA 103403 151162 . - . ID=Smp_315690.1;geneID=Smp_315690
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 103441 103770 . - 0 Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 142981 143205 . - 0 Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 145395 145678 . - 2 Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 . - 0 Parent=Smp_315690.1
SM_V7_1 AUGUSTUS mRNA 103403 151162 . - . ID=Smp_315690.2;geneID=Smp_315690
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 105920 106144 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 106876 107159 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 140582 140849 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 103441 103770 . - 0 Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 105920 106144 . - 0 Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 106876 107159 . - 2 Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 140582 140849 . - 0 Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 . - 0 Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 145395 145678 . - 2 Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 151075 151132 . - 0 Parent=Smp_315690.2
Example 2#
This test is based on the file used by GFF3sort
The GFF file to sort#
##gff-version 3
###
A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;description=Novel: Intergenic transcript
A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41
###
A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;description=Novel: Intergenic transcript
A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42
Results#
AGAT#
AGAT v0.9.0
- default sorting
agat_convert_sp_gxf2gxf.pl --gff test2.gff --merge_loci
##gff-version 3
###
A01 Cufflinks gene 473 6386 . - . ID=nbisL1-mrna-1;description=Novel: Intergenic transcript
A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;Parent=nbisL1-mrna-1;description=Novel: Intergenic transcript
A01 Cufflinks exon 473 814 . - . ID=exon-1;Parent=XLOC_001154.41
A01 Cufflinks exon 1626 2574 . - . ID=exon-2;Parent=XLOC_001154.41
A01 Cufflinks exon 2695 2721 . - . ID=exon-3;Parent=XLOC_001154.41
A01 Cufflinks exon 3637 3726 . - . ID=exon-4;Parent=XLOC_001154.41
A01 Cufflinks exon 5329 5408 . - . ID=exon-5;Parent=XLOC_001154.41
A01 Cufflinks exon 5994 6154 . - . ID=exon-6;Parent=XLOC_001154.41
A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;Parent=nbisL1-mrna-1;description=Novel: Intergenic transcript
A01 Cufflinks exon 473 2024 . - . ID=exon-7;Parent=XLOC_001154.42
A01 Cufflinks exon 2615 2721 . - . ID=exon-8;Parent=XLOC_001154.42
A01 Cufflinks exon 3637 3726 . - . ID=exon-9;Parent=XLOC_001154.42
A01 Cufflinks exon 5329 6386 . - . ID=exon-10;Parent=XLOC_001154.42
- Tabix sorting
agat_convert_sp_gxf2gxf.pl --gff test2.gff --merge_loci --tabix
##gff-version 3
###
A01 Cufflinks gene 473 6386 . - . ID=nbisL1-mrna-1;description=Novel: Intergenic transcript
A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;Parent=nbisL1-mrna-1;description=Novel: Intergenic transcript
A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;Parent=nbisL1-mrna-1;description=Novel: Intergenic transcript
A01 Cufflinks exon 473 814 . - . ID=exon-1;Parent=XLOC_001154.41
A01 Cufflinks exon 473 2024 . - . ID=exon-7;Parent=XLOC_001154.42
A01 Cufflinks exon 1626 2574 . - . ID=exon-2;Parent=XLOC_001154.41
A01 Cufflinks exon 2615 2721 . - . ID=exon-8;Parent=XLOC_001154.42
A01 Cufflinks exon 2695 2721 . - . ID=exon-3;Parent=XLOC_001154.41
A01 Cufflinks exon 3637 3726 . - . ID=exon-4;Parent=XLOC_001154.41
A01 Cufflinks exon 3637 3726 . - . ID=exon-9;Parent=XLOC_001154.42
A01 Cufflinks exon 5329 5408 . - . ID=exon-5;Parent=XLOC_001154.41
A01 Cufflinks exon 5329 6386 . - . ID=exon-10;Parent=XLOC_001154.42
A01 Cufflinks exon 5994 6154 . - . ID=exon-6;Parent=XLOC_001154.41
GenomeTools#
GenomeTools 1.6.1
gt gff3 -sortlines -tidy -retainids test2.gff
##gff-version 3
##sequence-region A01 473 6386
A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42
A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;description=Novel: Intergenic transcript
A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;description=Novel: Intergenic transcript
A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41
###
gt gff3 -retainids test2.gff
##gff-version 3
##sequence-region SM_V7_1 103403 151162
SM_V7_1 AUGUSTUS gene 103403 151162 0.12 - . ID=Smp_315690
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.02 - . ID=Smp_315690.1;Parent=Smp_315690
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 103441 103770 0.93 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.1.cds;Parent=Smp_315690.1
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.1
SM_V7_1 AUGUSTUS mRNA 103403 151162 0.1 - . ID=Smp_315690.2;Parent=Smp_315690
SM_V7_1 AUGUSTUS three_prime_UTR 103403 103440 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 103403 103770 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 103441 103770 0.96 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 105920 106144 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 105920 106144 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 106876 107159 0.93 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 106876 107159 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 140582 140849 0.85 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 140582 140849 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 142981 143205 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 142981 143205 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 145395 145678 1 - 2 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 145395 145678 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS CDS 151075 151132 1 - 0 ID=Smp_315690.2.cds;Parent=Smp_315690.2
SM_V7_1 AUGUSTUS exon 151075 151162 . - . Parent=Smp_315690.2
SM_V7_1 AUGUSTUS five_prime_UTR 151133 151162 . - . Parent=Smp_315690.2
###
GFF3sort#
GFF3sort 0.1.a1a2bc9
gff3sort.pl --precise test2.gff
##gff-version 3
A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;description=Novel: Intergenic transcript
A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;description=Novel: Intergenic transcript
A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41
gffread#
gffread v0.11.4
gffread test2.gff
# gffread test2.gff
# gffread v0.11.4
##gff-version 3
A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41
A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41
A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41
A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42
A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42
A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42