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felixgrunberger / microbepore

This is the repository for the manuscript “Expanding the transcriptomic toolbox in prokaryotes by Nanopore sequencing of RNA and cDNA molecules.” In this study, we applied and benchmarked all currently available RNA-seq kits from Oxford Nanopore technologies to analyse RNAs in the prokaryotic model organism Escherichia coli K-12.
https://felixgrunberger.github.io/microbepore
MIT License
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ModuleNotFoundError: No module named 'idr' : termseq-peaks #4

Open ramnageena11 opened 2 years ago

ramnageena11 commented 2 years ago

Hi Felix, Got an error while ran the script for calling the peaks.

$ termseq_peaks /media/majorram/Analysis_Data/singhrn/transcriptome_atlas/tss/trimmed/output/barcode07.plus.bedgraph /media/majorram/Analysis_Data/singhrn/transcriptome_atlas/tss/trimmed/output/barcode08.plus.bedgraph /media/majorram/Analysis_Data/singhrn/transcriptome_atlas/tss/trimmed/output/barcode09.plus.bedgraph --peaks /media/majorram/Analysis_Data/singhrn/transcriptome_atlas/tss/trimmed/output/barcode789.plus.peaks --strand + Traceback (most recent call last): File "/home/majorram/anaconda3/bin/termseq_peaks", line 11, in from peaklib.peaklib import idr_peak_calls File "/home/majorram/anaconda3/lib/python3.9/site-packages/peaklib/peaklib.py", line 6, in from idr import idr ModuleNotFoundError: No module named 'idr'

felixgrunberger commented 2 years ago

I recommend looking into the documentation of the tmerseq_peaks package (https://github.com/NICHD-BSPC/termseq-peaks). Maybe installing the python module by pip install idr helps (if you installed termseq_peaks via pip).

ramnageena11 commented 2 years ago

Hi Felix, I tried as you suggested. It says idr is already there.

$ pip install idr Requirement already satisfied: idr in ./anaconda3/lib/python3.9/site-packages (0.0.1)

ianzhao2022 commented 11 months ago

Please install the idr with conda, with pip install you might install a different version of idr. conda install idr