explicit error when CELLEX input does not contain human Ensembl gene IDs

[pascaltimshel]

CELLECT does not give a helpful error when CELLEX input does not contain human Ensembl gene IDs.

See also 'Explicit failure when no genes found ' #40

Current error when CELLEX input does not contain human Ensembl gene IDs, but e.g. human gene symbols:

[Fri Feb 21 11:25:08 2020]
Error in rule format_and_map_genes:
    jobid: 136
    output: /sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/CELLECT-LDSC-EXAMPLE/precomputation/humanfetal-test/bed/humanfetal-test.Mural-Mural.bed
    log: /sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/CELLECT-LDSC-EXAMPLE/logs/log.format_and_map_snake.humanfetal-test.Mural-Mural.txt (check log file(s) for error message)
    conda-env: /sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/.snakemake/conda/216cc198
 
Traceback (most recent call last):
  File "/sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/.snakemake/scripts/tmp8h_l2txa.format_and_map_snake.py", line 111, in <module>
    multi_gene_sets_to_dict_of_beds(df_multi_gene_set_human, df_gene_coords, windowsize, bed_out_dir + '/tmp', bed_out_dir, out_prefix)
  File "/sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/.snakemake/scripts/tmp8h_l2txa.format_and_map_snake.py", line 92, in multi_gene_sets_to_dict_of_beds
    bed_for_annot = pybedtools.BedTool(list_of_lists).sort().merge(c=[4,5], o=["distinct","max"])
  File "/sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/.snakemake/conda/216cc198/lib/python3.6/site-packages/pybedtools/bedtool.py", line 917, in decorated
    result = method(self, *args, **kwargs)
  File "/sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/.snakemake/conda/216cc198/lib/python3.6/site-packages/pybedtools/bedtool.py", line 401, in wrapped
    decode_output=decode_output,
  File "/sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/.snakemake/conda/216cc198/lib/python3.6/site-packages/pybedtools/helpers.py", line 455, in call_bedtools
    raise BEDToolsError(subprocess.list2cmdline(cmds), stderr)
pybedtools.helpers.BEDToolsError:
Command was:
 
                bedtools merge -o distinct,max -i /sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/CELLECT-LDSC-EXAMPLE/precomputation/humanfetal-test/bed/tmp/pybedtools.ziydjb7y.tmp -c 4,5
 
Error message was:
 
*****
***** ERROR: Requested column 4, but database file /sc/orga/projects/loosr01a/daiane/projects/scRNAseq/CELLECT/CELLECT-LDSC-EXAMPLE/precomputation/humanfetal-test/bed/tmp/pybedtools.ziydjb7y.tmp only has fields 1 - 0.