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Description
I have a genome fasta file, gff file. I want to generate the genbank format file to train with Augustus.
My fasta file likes this.
Scaffold_1;HRSCAF=1
GAGTGAGAGGATGGAAACGGTGAAACCGTGGGTGGGAGGGGTAGTTTCTGGTTTCGGGATGGTTTTCGGTTATTGTGGGCGAGGGTGTGCTGGAAGAGAGAGAGAGAGTGATGACGAGGTAGAGAGAGAAGCGGGGCGAAGATGGGCATGGAGGTGTTCTAGGTATGGCGAAACGAAGGTCTGGGTTCTTAGGGTTGGGTATCGGGGAGAGAGAAAGCGAATAAGAGAGAGAAAGTGCGTGAGAAGGGAAGGGGGGTTTAAAACGCGAACCGGTTCACTTACTGAACCGGGCCGGCCCGGTTCAACAAACCGGTCTGGCCCGGTTCAACAAACCGGTCTGGTTTCTTTTTTTTTTTCTATTTTTCCTCACATCTGAACCGGTTTTTAGAATTTGGCCCGGTTATTCAACCTCCGACATTTCTTCTATTTTTTTTCGCTTTTTCCGCCATTTAAGCCCATTTTTTGCATTTATTCAAAATCTGCAAAATAAAATAAAATCAATTAAAAACCCTAAAAATATTATTAAAACAAGCCTAAAATTGGTGGAAAAGTATCTTAAAAATATCACATTTTTGGCTCAAACAGGGGTTACCGTGGGCTGGGTGGTTTCTGGGTTTGGGAAGGGAGTGTGCTGGAGGAGAGAGAGAGATGACGAGGTAGAGAGAGAGTGGGCATCGCGATTCGAAGGTTCTGGGTTTCTAGGGTTTCCTGAACGGGGTCGGGGAAGCAGAGGACGCGAACCAGGAAGAAGAAGAAAGGAGACGCGAGAAAGGGGAGGGGGGTGTTTTAAGTGAGAACCGGTTCACGCGAACCGGTTTGCTGAACCGGACCGGTCCGGTTCAACTGGACCGGTCTGGTTTTTTTCCTTCTTCTTTCTTTGGCCGGTTTTTATCAATTTT
gff file generate by StringTie likes this:
Scaffold_15;HRSCAF=18| StringTie| transcript| 1| 558|1000| .| .| gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "11.043011"; FPKM "0.745167"; TPM "1.132539";
Scaffold_15;HRSCAF=18| StringTie| exon| 1| 558|1000| .| .| gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "11.043011";
Scaffold_91;HRSCAF=104| StringTie| transcript| 220|493|1000| .| .| gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "3.656934"; FPKM "0.246765"; TPM "0.375045";
The command:
gff2gbSmallDNA.pl stringtie.gff ~/ncbi/public/sra/hylocereus_undatus_05Mar2019_MZjug.fasta 100 string.gb
However, I get nothing.