Fix plugin path in command line output

[nuno-agostinho]

Currently, the VEP command-line in output is hiding all plugin parameters preceding a path delimiter (/ or \).

For instance, if we run multiple plugins with a command like:

./vep --i $vcf \
      --cache homo_sapiens/tabixconverted/ \
      --plugin dbNSFP,dbNSFP/4.4a/dbNSFP4.4a_grch38.gz,rs_dbSNP \
      --plugin GO,plugin_data/GO_data_files/ \
      --plugin DisGeNET,file=DisGeNET/May_2020/all_variant_disease_pmid_associations_final.tsv.gz

The output will be:

## VEP command-line: vep --cache [PATH]/ --input_file [PATH]/A530_small.vcf --offline --output_file [PATH]/vep-output.txt --plugin [PATH]/all_variant_disease_pmid_associations_final.tsv.gz

Change log

• Fix command plugin path hiding parameters for multiple plugins
• Use lookahead to avoid stripping the directory path if finishing with /: for instance, homo_sapiens/tabixconverted/ will become [PATH]/tabixconverted/
• Simplify code

Testing

The output should be similar to:

## VEP command-line: vep --dir_cache [PATH]/tabixconverted/ --fasta [PATH]/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --force_overwrite --input_file [PATH]/A530_small.vcf --offline --output_file [PATH]/vep-output.txt --plugin dbNSFP,[PATH]/dbNSFP4.4a_grch38.gz,rs_dbSNP --plugin GO,[PATH]/GO_data_files/ --plugin DisGeNET,file=[PATH]/all_variant_disease_pmid_associations_final.tsv.gz

[nakib103]

Looks good!