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chapmanb
Incubator for useful bioinformatics code, primarily in Python and R
There are small typos in: - posts/conferences/bosc2018_day1a.md - posts/seminars/tumor_heterogeneity_carter.md Fixes: - Should read `suppressors` rather than `supressors`. - Should read `service` rather than `serivce`. Semi-automated pull request generated by https://github.com/timgates42/meticulous/blob/master/docs/NOTE.md
Hi, Thank you for this very useful script!! I was wondering if it's possible to create the protein multi fasta file with the order of ref_file (contigs) instead of the...
Hi, I'd like to add this issue for those who'd like to use the script with an alternative codon table. Example: If you want to translate the sequence with a...
I was just wondering if it would be possible for a new release of the gff package to be made sometime soon. The fix from #126 would be really nice...
Hi! I annotated a bacterium (_Acidipropionibacterium acidipropionici_ - strain FAM19036) with [NCBI PGAP](https://github.com/ncbi/pgap). I wanted to create SeqIO-objects from the gff file, but it failed: ```python3 import pprint from BCBio...
I'm trying to parse a gff file downloaded from NCBI (GCA_001536265) and when I iterate on the parser it gives me this error `Did not find remapped ID location: gene670,...
Hi, Came across a issue after using gff2_to_gff3.py script on a gff from GIGA DB. Steps to reproduce. wget -c ftp://climb.genomics.cn/pub/10.5524/100001_101000/100028/PigeonPea_V5.0.gene.gff.gz python bcbb/gff/Scripts/gff/gff2_to_gff3.py PigeonPea_V5.0.gene.gff gff3ToGenePred PigeonPea_V5.0.gene.gff3 PigeonPea_V5.0.gene.genePred (gff3ToGenePred is from...
Discovered that GFF module supports writing out sequences with IDs that don't parse correctly on reading. If you submit a record to GFF for writing which has an ID which...
Just filing it since even though this library doesn't seem to see a lot of activity lately. Script: ``` python #!/usr/bin/env python import sys from BCBio import GFF from Bio...