I would suggest to useagat_convert_sp_gff2gtf.plfromAGATbecause you loose information withgffread. e.g here a gff example: ##gff-version 3scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2scaffold625 maker transcript 337818 343277 . + . ID=CLUHART00000008717;Par...
pip install bcbio-gff 转换代码 Converting other formats to GFF3;只需要在脚本里面改成你的文件就可以了。 fromBCBioimportGFFfromBioimportSeqIOin_file="your_file.gb"out_file="your_file.gff"in_handle=open(in_file)out_handle=open(out_file,"w")GFF.write(SeqIO.parse(in_handle,"genbank"),out_...
Convert to genomic coordinates, so individual protein hits can be seen spanning exons. The genes-gcan be defined using the GTF output of StringTie. blast2genomegff.py -b stringtie_vs_swissprot_blastx.tab -g stringtie.gtf -d uniprot_sprot.fasta -S > stringtie_vs_swissprot_blastx.gff ...
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. - bioconvert/bioconvert
Convert GTF/GFF2 to CSV for your convenience, e.g. insert it into a database or load it into pandas dataframe for slicing and dicing.DownloadI have converted multiple versions of gtf files for the human genome, and the gtf files across multiple species in Ensembl release 93 to csv files...
as GFF3, GTF, etc. Users interested in using a mix of files downloaded from different sources and use them in a single pipeline may end up with seq-id mismatch related errors. This script converts seq-ids from one style to the other in order to make the files compatible with each ...
Then run with theAUGUSTUSGFF (ensure this is GFF format and not GTF), instructing to use CDS features as exons with-x. Depending on version, theAUGUSTUSoutput might appear as below, where ID is not explicitly given in the attributes of the gene or transcripts (it just saysg1), but is ...