scored bed file format
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Hi,
This is a sample of my scored bed file
chr12 97061051 97062237 merged_10 -0.245689838393023 . chr2 57629190 57630191 merged_100 -0.157350109304036 . chr6 100838637 100839876 merged_1000 4.78625104090801 .
This is the error I get. Not sure what I'm doing wrong here. The bed file is 6 columns with the last 2 being score and score and strand
importing peak data 2021-08-18 18:17:54.689990 Traceback (most recent call last): File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/bin/meirlop", line 11, in <module> sys.exit(main()) File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/lib/python3.7/site-packages/meirlop/__main__.py", line 27, in main args.func(args) File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/lib/python3.7/site-packages/meirlop/__main__.py", line 328, in run_meirlop revcomp = revcomp) File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/lib/python3.7/site-packages/meirlop/motif_enrichment.py", line 55, in analyze_scored_fasta_data_with_lr in peak_sequence_dict.keys()} File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/lib/python3.7/site-packages/meirlop/motif_enrichment.py", line 54, in <dictcomp> for sequence_id KeyError: 'merged_10::chr12:97061051-97062237'
I tried to run using a Fasta file instead of a bed file. I get similar error
importing peak data 2021-08-20 17:53:38.874099 Traceback (most recent call last): File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/bin/meirlop", line 11, in <module> sys.exit(main()) File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/lib/python3.7/site-packages/meirlop/__main__.py", line 27, in main args.func(args) File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/lib/python3.7/site-packages/meirlop/__main__.py", line 328, in run_meirlop revcomp = revcomp) File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/lib/python3.7/site-packages/meirlop/motif_enrichment.py", line 55, in analyze_scored_fasta_data_with_lr in peak_sequence_dict.keys()} File "/broad/rosenlab_archive/Software/meirlop-0.0.16/miniconda3/envs/myenv/lib/python3.7/site-packages/meirlop/motif_enrichment.py", line 54, in <dictcomp> for sequence_id KeyError: 'chr12:97061451-97061837'
Used nameOnly option to get the Fasta file and scored the bed through the covariates. Worked out fine.