Skip to content

"AttributeError: Peak instance has no attribute 'peaks' " when plot peak overlaps instead of read density #9

@amdreamer

Description

@amdreamer

Hi, I'm trying to make metagene plot described in this example: https://github.com/YeoLab/rbp-maps/blob/c529fb694fadc130537d84c295a66723edc14ab3/examples/metagene/run_metagene_551_01.sh.

Here is my scripts

CDS=/data/DDX6_eClip/11_metaGene/gencode.v37.basic.annotation_201.eCLIP_upProtein.CDS.bed
UTR5=/data/DDX6_eClip/11_metaGene/gencode.v37.basic.annotation_201.eCLIP.fiveUTRs.bed
UTR3=/data/DDX6_eClip/11_metaGene/gencode.v37.basic.annotation_201.eCLIP.threeUTRs.bed

peak=/data/DDX6_eClip/combineRep1Rep2.compressed.bed.sorted.bb

plot_map \
--peak ${peak} \
--event metagene \
--normalization_level 0 \
--annotations ${CDS} ${UTR3} ${UTR5} \
--annotation_type cds 3utr 5utr \
--output CLIP_gene.metagene.svg

The peak file is sorted bigbed format. The following is the error message:
[bwHdrRead] There was an error while reading in the header! [pyBwOpen] bw is NULL! 0%| | 0/41 [00:00<?, ?it/s]Traceback (most recent call last): File "/work/bio-wangmr/.conda/envs/rbp-map/bin/plot_map", line 11, in <module> load_entry_point('rbp-maps==0.1.4', 'console_scripts', 'plot_map')() File "build/bdist.linux-x86_64/egg/maps/plot_map.py", line 548, in main File "build/bdist.linux-x86_64/egg/maps/plot_map.py", line 104, in run_make_peak File "build/bdist.linux-x86_64/egg/density/Map.py", line 1076, in create_matrices File "build/bdist.linux-x86_64/egg/density/matrix.py", line 184, in meta File "build/bdist.linux-x86_64/egg/density/intervals.py", line 774, in generic_site File "build/bdist.linux-x86_64/egg/density/Peak.py", line 100, in values AttributeError: Peak instance has no attribute 'peaks'

Thanks!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions