"AttributeError: Peak instance has no attribute 'peaks' " when plot peak overlaps instead of read density
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Description
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!
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the metagene example command and the traceback through density/intervals.py and density/Peak.py, especially Peak.values. Check how the supplied sorted bigBed peak file is opened and represented before the failing call. Done means the command completes without the AttributeError and produces the requested metagene SVG.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100