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_...
blast2gff.py clean_gff.py collate_features.py draw_annotation_blocks.R draw_genome_annotation.R draw_protein_gtf.R extract_coordinates.py make_parent_features.py microsynteny.py microsynteny_to_ortho_pairs.py number_contigs_by_length.py
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. - bioconvert/bioconvert
options.stdout.write("%s\n"% str(y))elif"merge-genes"== options.method:# merges overlapping genes#gffs = GTF.iterator_sorted_chunks( GTF.flat_gene_iterator(GTF.iterator(options.stdin)), sort_by="contig-strand-start")defiterate_chunks(gff_chunks):last = gff_chunks.next() to_join = [...
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 ...
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 ...