GEO Collector

Description

GEOcollector is a Python package for collecting metadata about gene expression datasets from the NCBI Gene Expression Omnibus (GEO) database. It will convert a list of GSM accession numbers and cell types into the information required for FastqToGeneCounts to process the raw RNA-seq data.

Long story short, given an input file like this:

GSM,cell_type
GSM3785334,baso
GSM3898581,baso

GEOcollector will output a file like this (without formatted columns):

GSE       ,GSM        ,SRR        ,Rename    ,Strand ,Prep Method ,Platform Code ,Platform Name                      ,Source           ,Cell Characteristics                                                                                                                                                                                                                        ,Replicate Name                                                        ,Strategy ,Publication ,Extra Notes
GSE131525 ,GSM3785334 ,SRR9097791 ,baso_S1R1 ,SE     ,total       ,GPL16791      ,Illumina HiSeq 2500 (Homo sapiens) ,B                ,subject - disease status: Screened Healthy Control;subject: HC3;age at draw: 55;Sex: Female;median cv coverage: 0.763618;fastq total reads: 6241803;unpaired reads examined: 5663490;unpaired read duplicates: 1597507;primary race: White; ,lib3945                                                               ,RNA-Seq  ,31671072    ,
GSE133028 ,GSM3898581 ,SRR9328889 ,baso_S2R1 ,PE     ,total       ,GPL20301      ,Illumina HiSeq 4000 (Homo sapiens) ,peripheral blood ,cell type: peripheral blood B cells;                                                                                                                                                                                                        ,Patient 2 IgD-CD27- double negative B cells from the peripheral blood ,RNA-Seq  ,32859762    ,
GSE133028 ,GSM3898591 ,SRR9328899 ,baso_S2R2 ,PE     ,total       ,GPL20301      ,Illumina HiSeq 4000 (Homo sapiens) ,peripheral blood ,cell type: peripheral blood B cells;                                                                                                                                                                                                        ,Patient 3 IgD-CD27- double negative B cells from the peripheral blood ,RNA-Seq  ,32859762    ,

Installation

To install GEOcollector, you can use pip:

pip install GEOcollector

Usage

The following sections are command line parameters associated with GEOcollector

Command Line Interface

To execute GEOcollector, simply call it from the command line with the relevant parameters

geocollector --api-key APIKEY --input-file /home/user/input.csv --verbose
geocollector --input-file /home/user/input.csv --quiet
geocollector --api-key APIKEY --input-file /home/user/input.csv

To view help for GEOcollector, run the following command

geocollector --help

API Key

Without an API key, NCBI limits the number of requests to 3 per second. With an API key, this value is increased to 10 requests per second. To obtain an API key, follow the below steps

1. Access NCBI's website
2. Click "Log In" in the top right corner
   1. If you do not have an account, create one now
3. Click your username in the top right corner
4. Click "Account settings" in the dropdown menu
5. Scroll down to the "API Key" section
6. Click "Create API Key"
7. Copy the API key that has been created

Input file

The input file should be a CSV file in the following format. Multiple GSMs can be associated to a single cell type

GSM,cell_type
GSM_1,cell_type_1
GSM_2,cell_type_1
GSM_3,cell_type_1
GSM_4,cell_type_2

Verbosity

If you would like to show debug information on the command line, pass the flag --verbose. If you would like to silence all output (except warnings), pass the flag --quiet. If neither flag is passed, standard "info" messages will be shown

If you have problems, please create a new issue