modbamtools
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rrazaghi
Set of tools to manipulate and visualize modified base bam files
Hi all, I'm using the modbamtools for my annotated nanopore sequences and faced the index error of my gtf.gz.tbi file. I'm pretty sure the positions are in the right range....
I received this error when trying to add a bed track for a batched run ```File "/XXXXX/miniconda3/envs/202209_cyp2d6_revisited/lib/python3.9/site-packages/modbamtools/tracks_webgl.py", line 242, in get_tracks_gl elements = parse_bed_rectangle_gl(bed, chrom, start, end) NameError: name 'parse_bed_rectangle_gl'...
Hi, I am using modbamtools to view methylation of a region of interest and ran the following command: ``` modbamtools plot \ -r :- \ -b .bed \ -o \...
I installed modbamtools with pip but except for the plot command, it doesn't seem to recognize any other. Even `modbamtools --help` only lists `plot` under commands ``` Usage: modbamtools [OPTIONS]...
`-ht` doesn't run if a GTF is not provided. # Runs `modbamtools plot --batch genes.bed --gtf gencode.v38.annotation.sorted.gtf.gz -ht --cluster --prefix test_batch_hp_removed_gm12878_batch --samples GM12878 --track-titles Genes --out . hp_removed_gm12878_ul_sup_megalodon_chr20.bam` # Does...
~pip install modbamtools ERROR: Ignored the following versions that require a different python version: 0.1.0 Requires-Python >=3.6, =3.6, =3.6, =3.6, =3.6, =3.8, =3.8, =3.8, =3.8, =3.8, =3.8, =3.8, =3.8, =3.8,...
modbamtools plot -r mtDNA:1-16626 --gtf /cluster/projects/nn9337k/as1_nanopolish/all_context/sequence.sorted.gtf.gz --out . --prefix unmethylated --samples unmethylated --track-titles Genes unmethylated.bam Traceback (most recent call last): File "/cluster/projects/nn9337k/anaconda/envs/modbamtools/bin/modbamtools", line 8, in sys.exit(cli()) File "/cluster/projects/nn9337k/anaconda/envs/modbamtools/lib/python3.8/site-packages/click/core.py", line 1130,...
My code is this: modbamtools plot -r NC_007793.1:607408-609562 95_0_0.bam -o modbamtools/ And my version is this: modbamtools --version : modbamtools, version 0.4.8 But I still have the issue with these...
Hi, I was trying to install modbamtools/0.4.8 on python/3.10, and found that libmodbampy is lacking. But installing on python/3.9 is fine. Since libmodbampy is part of modbampy, not sure if...
modbamtools plot command will append on more output if the same prefix is used. This could cause major issues when trying to optimize a plot. ## Example - these two...