GRASP Console Script

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	0.3.0b1

Last modified: 2016-10-17 00:18

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]
                  {phenotypes,phenotype_categories,all,population_flags,populations,study_columns,snp_columns}

Positional arguments:

display

Choice of item to display, if all, results are written to independant rst files, and optional args are ignored Possible choices: phenotypes, phenotype_categories, all, population_flags, populations, study_columns, snp_columns

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