Check specificity input for numeric values only

[pascaltimshel]

Problem

Print more informative error messages if the specificity input matrix is not all numeric.

Solution

Ensure that the specificity matrix:

1. can be parsed/read (using pandas)
2. contains all numeric values (no characters etc)
3. possibly additional checks...

Appendix

Example (semi cryptic) error message if specificity input contains characters values (and/or missing values?)

[Thu Jan  7 16:15:57 2021]
Error in rule make_annot:
    jobid: 299
    output: /opt/projects/data_processed.LIMITED_BACKUP/CELLECT_out/CELLECT-LDSC/precomputation/DATASETagg_copd_celltype/DATASETagg_copd_celltype.COMBINED_ANNOT.15.anno
t.gz
    log: /opt/projects/data_processed.LIMITED_BACKUP/CELLECT_out/CELLECT-LDSC/logs/log.make_annot_snake.DATASETagg_copd_celltype.15.txt (check log file(s) for error message)
    conda-env: /opt/software/pnt/CELLECT/.snakemake/conda/765b9fea

RuleException:
CalledProcessError in line 259 of /opt/software/pnt/CELLECT/cellect-ldsc.snakefile:
Command 'source /home/pnt/anaconda3/bin/activate '/opt/software/pnt/CELLECT/.snakemake/conda/765b9fea'; set -euo pipefail;  python /opt/software/pnt/CELLECT/.snakemake/scripts/tmpwj1v708y.mak
e_annot_from_geneset_all_chr_snake.py' returned non-zero exit status 1.
  File "/home/pnt/anaconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2231, in run_wrapper
  File "/opt/software/pnt/CELLECT/cellect-ldsc.snakefile", line 259, in __rule_make_annot
  File "/home/pnt/anaconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 560, in _callback
  File "/home/pnt/anaconda3/envs/snakemake/lib/python3.9/concurrent/futures/thread.py", line 52, in run
  File "/home/pnt/anaconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 546, in cached_or_run
  File "/home/pnt/anaconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2262, in run_wrapper
Traceback (most recent call last):
  File "/opt/software/pnt/CELLECT/.snakemake/scripts/tmps30nn0av.make_annot_from_geneset_all_chr_snake.py", line 299, in <module>
    dict_of_beds = map_ES_values_to_genes(overlap_df, specificity_df)
  File "/opt/software/pnt/CELLECT/.snakemake/scripts/tmps30nn0av.make_annot_from_geneset_all_chr_snake.py", line 87, in map_ES_values_to_genes
    max_ES_vals_dict[cell_type] = pybedtools.bedtool.BedTool.from_dataframe(get_max_ES_vals(chr_overlap_df, cell_type_ES_dict))
  File "/opt/software/pnt/CELLECT/.snakemake/scripts/tmps30nn0av.make_annot_from_geneset_all_chr_snake.py", line 63, in get_max_ES_vals
    max_ES_val = np.max(ES_val_list)
  File "/opt/software/pnt/CELLECT/.snakemake/conda/765b9fea/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 2505, in amax
    initial=initial)
  File "/opt/software/pnt/CELLECT/.snakemake/conda/765b9fea/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
TypeError: cannot perform reduce with flexible type