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CostaLab / reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
https://reg-gen.readthedocs.io/
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Issue Promoter Test #201

Open Galadrast85 opened 2 years ago

Galadrast85 commented 2 years ago

Hi I have problems with the promoter_test that gives me this error

***** Promoter Test **** * Input RNA sequence: /home/bioinfo/rgtdata/Loc100420879/Loc100420879.fasta * Output directory: Loc100420879/promoter_test/Loc100420879 Step 1: Calculate the triplex forming sites on RNA and DNA. Dump to file: tdf.dump.hg19.total_genes Running time: 0:03:24 Step 2: Calculate the frequency of DNA binding sites within the promoters. Counting frequency of promoters on DBD... 158 Binding target promoters 57 Binding non-target promoters Counting frequency of binding sites on DBD... 158 Binding sites on de promoters Traceback (most recent call last): File "/home/bioinfo/.local/bin/rgt-TDF", line 8, in sys.exit(main()) File "/home/bioinfo/.local/lib/python3.8/site-packages/rgt/tdf/Main.py", line 354, in main stat.count_frequency_promoters(target_regions=tdf_input.dna.target_regions, File "/home/bioinfo/.local/lib/python3.8/site-packages/rgt/tdf/Statistics.py", line 129, in count_frequency_promoters self.promoter["nde"]["dbs"][p.toString()] = counts[i] IndexError: list index out of range**

Where am I wrong? Thank you in advance

hyjforesight commented 2 years ago

Hello @Galadrast85 May I know how you ran through the rgt-motifanalysis matching? I met KeyError: "sequence 'chr22' not present" when running the tutorial. Thanks!

rgt-motifanalysis matching --organism hg19 --fpr 0.05 --input-files ~/RGT_MotifAnalysis_FullSiteTest/input/regions_K562.bed ~/RGT_MotifAnalysis_FullSiteTest/input/background.bed --output-location ~/RGT_MotifAnalysis_FullSiteTest/motif_matching/