gff2tbl

[stanislasmorand]

Dear Geo Pertea,
I have tried to use your script gff2tbl but encountered an Error message. First I only provided a gff file containing the fasta sequence. However gff2tbl requires a separate fasta file.

[15:03] morands@frrdcim20: gscripts-master $ ./gff2tbl pSE4_prokka.gff
Usage:
 gff2tbl -f <fasta_file> [-m <id2acc_map>] [-t <track>] [-o <out_prefix>]
    [-c <lab_prefix> ] [-b dbname] [-L] [-x <exclude.lst>] [-G] [-n <organism_name>] <gff_file>

 Convert GFF to .fsa and .tbl files to be used by tbl2asn

 For -m option, <id2acc_map> is a 2-column file mapping the genomic sequence IDs
 from the input gff and fasta_file (1st column) to GenBank accessions (2nd column)
 Other options:
    -L   :  use locus attribute for transcripts in order to identify a "gene"
            and its boundaries
    -G   : also output <out_prefix>.gff for table2asn
 A fasta file is required!

I thus extracted the fasta section outside the gff file and reinitiated the command line. Unfortunately, the new attempt was unsuccessful.

15:07] morands@frrdcim20: gscripts-master $ ./gff2tbl -f pSE4.fasta pSE4_prokka.gff
Error: transcript ICN77_02481_gene not stored in ttbl hash!

I don't know what means the error message. I attached my fasta and gff small files if the issue is coming form my files.
Thanks in advance for your precious time & help.
Kindest regards,
Stan
pSE4.fasta.txt
pSE4_prokka.gff.txt