Gff fails to parse on basic Gff file

[Koeng101]

package main

import (
	"fmt"
	"github.com/koeng101/poly"
)

// Started at 4:44
// 5:00 finished downloading all files
// 5:07 discovered big bug with gb file parsing (give this to poly folks)

func main() {
	// Parse Genbank file
	//ct := poly.GetCodonTable(11)
	sequence := poly.ReadGff("data/Arthrospira_platensis.gff")
	for _, feature := range sequence.Features {
		if feature.Type == "CDS" {
			fmt.Println(feature)
		}
	}
	// Find associated uniprot numbers

	// Find associated Rhea reaction numbers

	// Find associated Rhea
}

Like #152 , koeng101/poly has an up-to-date io.go file.

Output

panic: runtime error: index out of range [2] with length 2

goroutine 1 [running]:
github.com/koeng101/poly.ParseGff(0xc000180000, 0x31b6e7, 0x31b6e8, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
        /home/koeng/go/pkg/mod/github.com/koeng101/[email protected]/io.go:160 +0xaf9
github.com/koeng101/poly.ReadGff(0x645b01, 0x1e, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
        /home/koeng/go/pkg/mod/github.com/koeng101/[email protected]/io.go:333 +0xb4
main.main()
        /home/koeng/go/src/github.com/koeng101/fun_spira_project/main.go:15 +0x4b
exit status 2

We should be able to parse this file. Arthrospira_platensis.gff.gz

[TimothyStiles]

And here I thought we'd never actually have someone use the gff parser.

[TimothyStiles]

@Koeng101 has this been solved yet?

[Koeng101]

No don't think so. I think I actually just solved the problem that was preventing me from using the raw genbank (which forced me to use gff). Maybe we should depreciate GFF for a while until we can get proper error handling on it? Or keep it, but note it is buggy or whatever.

[toothsy]

I think I have an idea how to go about it....

Problem

• here this is a snippet from gff.go, for the ./data/ecoli-mg1655.gff, in line 132 it is assumed that the second line is always a place for ##sequence-region

• 

• the file Arthrospira_platensis.gff has ##sequence-region on line 8,

  • 
  • on line 2, #!gff-spec-version 1.21 has only two items in the split array, hence we get the index out of bounds error

• thing is this specific gff file has more than 2 line of meta, which is causing the parser to fail