cmap/sig_curie_tool repository overview

Synopsis: sig_curie_tool [--help, -h] [--undef_action UNDEF_ACTION] [-o, --out OUT] [--runtests] [--rundemo] [--rpt RPT] [--create_subdir CREATE_SUBDIR] [--verbose VERBOSE] [--encode_url ENCODE_URL] [--config CONFIG] [--score SCORE] [--rank RANK] [--up UP] [--down DOWN] [--min_set_size MIN_SET_SIZE] [--platform PLATFORM] [--feature_id FEATURE_ID] [--metric METRIC] [--es_tail ES_TAIL] [--dataset DATASET] [--use_gctx USE_GCTX]

Positional Arguments:

Optional Arguments: --help, -h Show this help message and exit --undef_action UNDEF_ACTION Action to take if an undefined argument is encountered. Default is error. Options are {error|warn|ignore} -o, --out OUT Output path --runtests Execute functional and unit tests. Default is 0 --rundemo Run the tool with sample inputs. Default is 0 --rpt RPT Report folder prefix --create_subdir CREATE_SUBDIR Create subfolder within out for saving results. Default is 1 --verbose VERBOSE Print debugging messages. Default is 1 --encode_url ENCODE_URL Encode all input URLs. Default is 0 --config CONFIG Argument configuration file --score SCORE Dataset of differential viability scores --rank RANK Dataset of ranks corresponding to the score dataset --up UP Set(s) of UP cell lines --down DOWN Set(s) of DOWN cell lines --min_set_size MIN_SET_SIZE Minimum query set size. Sets with fewer members will be excluded. Default is 2 --platform PLATFORM . Default is pr500_cs5. Options are {pr500_cs5} --feature_id FEATURE_ID Feature Identifiers. Default is cell_iname. Options are {feature_id|cell_iname} --metric METRIC Similarity metric. Default is wtcs. Options are {wtcs|cs} --es_tail ES_TAIL Specify two-tailed or one-tailed statistic for enrichment metrics. Default is both. Options are {both|up|down} --dataset DATASET Pre-canned datasets that can be queried without specifying score and rank matrices individually. Default is pasg_pr500_bydose. Options are {custom|pasg_pr500_bydose} --use_gctx USE_GCTX Use binary GCTX format optimized for large datasets if true. Default is 0

Description: Examples:

% Run query on a pre-canned dataset using single sided queries with cell_inames 
as features	 
sig_curie_tool --dataset 'pasg_pr500_bydose' --up 'up.gmt' --es_tail 'up'
 
% Run query on a custom dataset using single-sided queries with pr500 
feature-ids	 
sig_curie_tool --score 'score.gct' --rank 'rank.gct' '--feature_id' 'pr500_id' 
--up 'up.gmt' --down 'down.gmt'