YeoLab / rbp-maps

splicing and feature maps for RBPs
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"AttributeError: Peak instance has no attribute 'peaks' " when plot peak overlaps instead of read density #9

Open amdreamer opened 3 years ago

amdreamer commented 3 years ago

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!