GFFtools-GX
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gfftools - Galaxy toolshed repository
Hi, the output of gff-to-gtf.py contains only exon features even if the input file is a complete GFF file with all features... Could you please fix this error? Thanks. Séverine
Hi, I'm wondering why you removed GFF-to-GBK from your tool list ? https://github.com/vipints/GFFtools-GX/commit/c99274597ef7856e7b89d1afbbef33bd04295722 One of my users want to use something like that. Thanks by advance
Hi Vipin, Thank you very much for the GFFtools scripts. However, when I run the command, `python gff_to_bed.py ref.gff3 > out2.bed` while converting gff3 to bed 12 format, I receive...
I noticed some weird error when converting a GFF to GTF with `gff_to_gtf.py`. This is the gene model in the original GFF: ``` scaffold_00034 JGI exon 1 472 . -...
I encountered this issue in converting GCF_000001405.33_GRCh38.p7_genomic.gff. ``` Traceback (most recent call last): File "/.../gff_to_bed.py", line 119, in __main__() File "/.../gff_to_bed.py", line 116, in __main__ writeBED(Transcriptdb) File "/.../gff_to_bed.py", line 55,...
There's a bug in the gff to gtf converter: ``` Deha2F_6 JGI exon 544121 545199 . - . gene_id "DEHA2F06138g"; transcript_id "DEHA2F06138g"; Deha2F_6 JGI CDS 544121 545199 . - 2...
Hi I encountered this while converting GCF_000001405.33_GRCh38.p7_genomic.gff. I got an error about a string and int value being passed as operands to the `-` operator. In gff_to_bed.py, line 90 is...
I'm trying to use gff_to_gtf.py to convert Potato genome v.4.03 annotation (http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml; precisely, this file: http://solanaceae.plantbiology.msu.edu/data/PGSC_DM_V403_genes.gff.zip) in gft ,and I'm getting this: > ~$ python scripts/GFFtools-GX/gff_to_gtf.py PGSC_DM_V403_genes.gff > PGSC_DM_V403_genes.gtf >...
