Hi everybody,

I have to convert the genebank file of my virus genome to a gtf file for the aligment of my reads with STAR. I tried different tools, which I found by google search, but I doesn't work unfortunately.

I tried to do it with a perl script I found, called genbank2gtf_mRNA.pl from genebank2gtf and I tried a python script, called gb2gtf.py from lpryszcz, but when using the perl script with a custom chromosome file, I get an empty gtf file and when I tried to use the python script, I get the error: "command didn't found".

Can someone maybe recommend a converter tool or platform which I could use?

And; the genebank file contains splice site annotation from genious, does the conversion translate these coordinates?

Any help is greatfully appreciated :)

Edited: data exemple and tools, I struggled with

My gb data looks something like that:

    > FEATURES             Location/Qualifiers
    >      repeat_region   552..634
    >                      /vntifkey="34"
    >                      /label=U5
    >      CDS             5830..8414
    >                      /vntifkey="4"
    >                      /label=TAT
    >                      /note="HIV-1 tat protein"
    >      splicing_signal 5934..5935
    >                      /vntifkey="38"
    >                      /label=SA4c
    >      splicing_signal 5952..5953
    >                      /vntifkey="38"
    >                      /label=SA4a
    >      splicing_signal 5958..5959
    >                      /vntifkey="38"
    >                      /label=SA4b
    >      CDS             8787..9407
    >                      /vntifkey="4"
    >                      /label=NEF
    >                      /note="HIV-1 nef protein"
    >      splicing_signal 5775..5776
    >                      /vntifkey="38"
    >                      /label=SA3
    >      splicing_signal 6045..6046
    >                      /vntifkey="38"
    >                      /label=SD4
    >      CDS             5969..8643
    >                      /vntifkey="4"
    >                      /label=REV
    >                      /note="HIV-1 rev protein"
    >      splicing_signal 5974..5975
    >                      /vntifkey="38"
    >                      /label=SA5
    >      CDS             2085..5096
    >                      /vntifkey="4"
    >                      /label=POL
    >                      /note="HIV-1 pol polyprotein;  (NH2-terminus uncertain)"
    >      CDS             5041..5619
    >                      /vntifkey="4"
    >                      /label=VIF
    >                      /note="HIV-1 vif protein"
    >      CDS             5559..5849
    >                      /vntifkey="4"
    >                      /label=VPR
    >                      /note="HIV-1 vpr protein"
    >      repeat_region   9529..9626
    >                      /vntifkey="34"
    >                      /label=R
    >                      /note="HIV-1 R repeat 3' copy"
    >      CDS             6061..6306
    >                      /vntifkey="4"
    >                      /label=VPU
    >                      /note="HIV-1 vpu protein"
    >      CDS             6221..8785
    >                      /vntifkey="4"
    >                      /label=ENV
    >                      /note="HIV-1 envelope polyprotein"
    >      splicing_signal 6602..6603
    >                      /vntifkey="38"
    >                      /label=(SA6)
    >      splicing_signal 6720..6721
    >                      /vntifkey="38"
    >                      /label=(SD5)
    >                      /note="Mutation von GT in anderen Isolaten zu  AT"
    >      splicing_signal 8367..8368
    >                      /vntifkey="38"
    >                      /label=SA7
    >      LTR             1..634
    >                      /vntifkey="19"
    >                      /label=5'_LTR
    >                      /note="HIV-1 5' LTR"
    >      repeat_region   454..551
    >                      /vntifkey="34"
    >                      /label=R
    >                      /note="HIV-1 R repeat 5' copy"
    >      intron          744..5776
    >                      /vntifkey="15"
    >                      /label=TAT/REV/NEF_I
    >                      /note="HIV-1 tat, rev, nef mRNA intron 1"
    >      misc_feature    5743..5744
    >                      /vntifkey="21"
    >                      /label=JNCTN_NY5/LAV
    >                      /note="HIV-1 isolate NY5 DNA end/HIV-1 isolate LAV DNA start"
    >      intron          6045..8368
    >                      /vntifkey="15"
    >                      /label=TAT_II
    >                      /note="HIV-1 tat cds intron 2"
    >      CDS             790..2292
    >                      /vntifkey="4"
    >                      /label=GAG
    >                      /note="HIV-1 gag polyprotein"
    >      insertion_seq   1186..1186
    >                      /vntifkey="14"
    >                      /label=p17/p24
    >      splicing_signal 4963..4964
    >                      /vntifkey="38"
    >                      /label=SD2
    >      splicing_signal 744..745
    >                      /vntifkey="38"
    >                      /label=SD1
    >      splicing_signal 4911..4912
    >                      /vntifkey="38"
    >                      /label=SA1
    >      splicing_signal 5464..5465
    >                      /vntifkey="38"
    >                      /label=SD3
    >      polyA_signal    9602..9607
    >                      /vntifkey="25"
    >                      /label=POLY_A
    >                      /note="HIV-1 mRNA polyadenlyation signal"
    >      splicing_signal 5388..5389
    >                      /vntifkey="38"
    >                      /label=SA2
    >      intron          6045..8368
    >                      /vntifkey="15"
    >                      /label=REV_II
    >                      /note="HIV-1 rev cds intron 2"
    >      intron          6045..8368
    >                      /vntifkey="15"
    >                      /label=TAT/REV/NEF_II
    >                      /note="HIV-1 tat, rev, nef mRNA intron 2"
    >      LTR             9076..9709
    >                      /vntifkey="19"
    >                      /label=3'_LTR
    >                      /note="HIV-1 3' LTR"
    >      misc_feature    5059..5060
    >                      /vntifkey="21"
    >                      /label=SD2b
    >      splicing_signal 8335..8336
    >                      /vntifkey="38"
    >                      /label=SA7a
    >      splicing_signal 8440..8441
    >                      /vntifkey="38"
    >                      /label=SA7b
    >      splicing_signal 4541..4542
    >                      /vntifkey="38"
    >                      /label=SA1a
    >      splicing_signal 4722..4723
    >                      /vntifkey="38"
    >                      /label=SD1a BASE COUNT     3423 a      1756 c      2364 g      2166 t  ORIGIN
    >         1 tggaa....


I think you can use GFF file with STAR aligner. 

https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

> 2.2.3 Annotations in GFF format. 

>In addition to the aforementioned options, for GFF3 formatted annotations you need to use
> --sjdbGTFtagExonParentTranscript Parent. In general, for --sjdbGTFfile files STAR only processes lines which have --sjdbGTFfeatureExon (=exon
> by default) in the 3rd field (column). The exons are assigned to the
> transcripts using parent-child relationship defined by the
> --sjdbGTFtagExonParentTranscript (=transcript id by default) GTF/GFF attribute.

If you would like to convert GFF3 to GTF then you can use gffread. 
Please look at this post for further details: https://www.biostars.org/p/45791/