GRASP Console ScriptΒΆ
A Simple GRASP (grasp.nhlbi.nih.gov) API based on SQLAlchemy and Pandas
Author | Michael D Dacre <mike.dacre@gmail.com> |
Organization | Stanford University |
License | MIT License, use as you wish |
Created | 2016-10-08 |
Version | 0.4.0b1 |
Last modified: 2016-10-18 00:38
This is the front-end to a python grasp api, intended to allow easy database creation and simple querying. For most of the functions of this module, you will need to call the module directly.
usage: grasp [-h] {search,conf,info,init} ...
- Sub-commands:
- search (s, lookup)
Query database for variants by location or id
Query for SNPs in the database. By default returns a tab-delimeted list of SNPs with the following columns: ‘id’, ‘snpid’, ‘study_snpid’, ‘chrom’, ‘pos’, ‘phenotype’, ‘pval’ The –extra flag adds these columns: ‘InGene’, ‘InMiRNA’, ‘inLincRNa’, ‘LSSNP’ The –study-info flag adds these columns: ‘study_id (PMID)’, ‘title’ The –db-snp flag uses the myvariant API to pull additional data from db_snp.
usage: grasp search [-h] [--extra] [--study-info] [--db-snp] [--pandas] [-o] [--path] query
- Positional arguments:
query rsID, chrom:loc or chrom:start-end - Options:
--extra Add some extra columns to output --study-info Include study title and PMID --db-snp Add dbSNP info to output --pandas Write output as a pandas dataframe -o, --out File to write to, default STDOUT. --path PATH to write files to
- conf (config)
Manage local config
usage: grasp conf [-h] [--db {sqlite,postgresql,mysql} | --get-path | --set-path PATH | --init]
- Options:
--db Set the current database platform.
Possible choices: sqlite, postgresql, mysql
--get-path Change the sqlite file path --set-path Change the sqlite file path --init Initialize the config with default settings. Will ERASE your old config!
- info
Display database info
Write data summaries (also found on the wiki) to a file or the console. Choices: all: Will write everything to separate rst files, ignores all other flags except `–path` phenotypes: All primary phenotypes. phenotype_categories: All phenotype categories. populations: All primary populations. population_flags: All population flags. snp_columns: All SNP columns. study_columns: All Study columns.
usage: grasp info [-h] [-o] [--path] {population_flags,study_columns,populations,phenotypes,snp_columns,all,phenotype_categories}
- Positional arguments:
display Choice of item to display, if all, results are written to independant rst files, and optional args are ignored
Possible choices: population_flags, study_columns, populations, phenotypes, snp_columns, all, phenotype_categories
- Options:
-o, --out File to write to, default STDOUT. --path PATH to write files to
- init
Initialize the database
usage: grasp init [-h] [-n] study_file grasp_file
- Positional arguments:
study_file GRASP study file from: github.com/MikeDacre/grasp/blob/master/grasp2_studies.txt grasp_file GRASP tab delimeted file - Options:
-n, --no-progress Do not display a progress bar