Hi, after testing with your GTF file, I found that featureCounts will throw this error when there are two fields with quotes in the "inference" part. In the ERROR message you posted above, there are"ab initio prediction:Prodigal:002006"and"similar to AA sequence:ISfinder:ISHaha5", and the...
python3 reform.py --chrom=<chrom> \ --position=<pos> \ --in_fasta=<in_fasta> \ --in_gff=<in_gff> \ --ref_fasta=<ref_fasta> \ --ref_gff=<ref_gff> Parameters chrom ID of the chromsome to modify position Position in chromosome at which to insert <in_fasta>. Can use -1...
to_join = [last]forgffsingff_chunks: d = gffs[0].start - last[-1].endifgffs[0].contig == last[0].contigand\ gffs[0].strand == last[0].strand:assertgffs[0].start >= last[0].start, \ ("input file should be sorted by contig, strand ""and position: d=%i:\nlast=\n%s...
parser.add_option("--input-filename-map", dest="input_filename_map", type="string", help="filename with a map of gene_ids to categories [default=None].") parser.add_option("--output-filename-synonyms", dest="output_filename_synonyms", type="string", help="output filename for syno...
("\t".join([transcript_id,str(num)])+"\n")defexon_pos(list_exon):print("--- Save the position info of each exon ---")count_exon={}forexoninlist_exon:transcript_id=exon.parentiftranscript_idincount_exon:cou
pfam2gff.py -g aug_nocomments_cds.gff -e 1e-3 -i aug_prots.pfam.tab -x > aug_prots_pfam.gff Produces the following example output. The results are not filtered by position, so it is evident that 3 different von Willebrand domains are found, though group 1 is clearly the strongest...
chr1- Output all features belongs to the reference sequence named "chr1". chr2:1000000- The region on "chr2" beginning at base position 1,000,000 and ending at the end of the chromosome. chr2:-2000- The region on "chr2" beginning at the start of the chromosome and ending at base...
pfam2gff.py -g aug_nocomments_cds.gff -e 1e-3 -i aug_prots.pfam.tab -x > aug_prots_pfam.gff Produces the following example output. The results are not filtered by position, so it is evident that 3 different von Willebrand domains are found, though group 1 is clearly the strongest...