usage reference
geofetch command-line usage instructions:
geofetch --help
usage: geofetch [<args>]
The example how to use geofetch (to download GSE573030 just metadata):
geofetch -i GSE67303 -m <folder> --just-metadata
To download all processed data of GSE57303:
geofetch -i GSE67303 --processed --geo-folder <folder> -m <folder>
Automatic GEO and SRA data downloader
options:
-h, --help show this help message and exit
-V, --version show program's version number and exit
-i INPUT, --input INPUT
required: a GEO (GSE) accession, or a file with a list
of GSE numbers
-n NAME, --name NAME Specify a project name. Defaults to GSE number
-m METADATA_ROOT, --metadata-root METADATA_ROOT
Specify a parent folder location to store metadata.
The project name will be added as a subfolder
[Default: $SRAMETA:]
-u METADATA_FOLDER, --metadata-folder METADATA_FOLDER
Specify an absolute folder location to store metadata.
No subfolder will be added. Overrides value of
--metadata-root.
--just-metadata If set, don't actually run downloads, just create
metadata
-r, --refresh-metadata
If set, re-download metadata even if it exists.
--config-template CONFIG_TEMPLATE
Project config yaml file template.
--pipeline-samples PIPELINE_SAMPLES
Optional: Specify one or more filepaths to SAMPLES
pipeline interface yaml files. These will be added to
the project config file to make it immediately
compatible with looper. [Default: null]
--pipeline-project PIPELINE_PROJECT
Optional: Specify one or more filepaths to PROJECT
pipeline interface yaml files. These will be added to
the project config file to make it immediately
compatible with looper. [Default: null]
--disable-progressbar
Optional: Disable progressbar
-k SKIP, --skip SKIP Skip some accessions. [Default: no skip].
--acc-anno Optional: Produce annotation sheets for each
accession. Project combined PEP for the whole project
won't be produced.
--discard-soft Optional: After creation of PEP files, all .soft files
will be deleted
--const-limit-project CONST_LIMIT_PROJECT
Optional: Limit of the number of the constant sample
characters that should not be in project yaml.
[Default: 50]
--const-limit-discard CONST_LIMIT_DISCARD
Optional: Limit of the number of the constant sample
characters that should not be discarded [Default: 250]
--attr-limit-truncate ATTR_LIMIT_TRUNCATE
Optional: Limit of the number of sample characters.Any
attribute with more than X characters will truncate to
the first X, where X is a number of characters
[Default: 500]
--add-dotfile Optional: Add .pep.yaml file that points .yaml PEP
file
--max-soft-size MAX_SOFT_SIZE
Optional: Max size of soft file. [Default: 1GB].
Supported input formats : 12B, 12KB, 12MB, 12GB.
--max-prefetch-size MAX_PREFETCH_SIZE
Argument to pass to prefetch program's --max-size
option, if prefetch will be used in this run of
geofetch; for reference: https://github.com/ncbi/sra-
tools/wiki/08.-prefetch-and-fasterq-dump#check-the-
maximum-size-limit-of-the-prefetch-tool
--silent Silence logging. Overrides verbosity.
--verbosity V Set logging level (1-5 or logging module level name)
--logdev Expand content of logging message format.
processed:
-p, --processed Download processed data [Default: download raw data].
--data-source {all,samples,series}
Optional: Specifies the source of data on the GEO
record to retrieve processed data, which may be
attached to the collective series entity, or to
individual samples. Allowable values are: samples,
series or both (all). Ignored unless 'processed' flag
is set. [Default: samples]
--filter FILTER Optional: Filter regex for processed filenames
[Default: None].Ignored unless 'processed' flag is
set.
--filter-size FILTER_SIZE
Optional: Filter size for processed files that are
stored as sample repository [Default: None]. Works
only for sample data. Supported input formats : 12B,
12KB, 12MB, 12GB. Ignored unless 'processed' flag is
set.
-g GEO_FOLDER, --geo-folder GEO_FOLDER
Optional: Specify a location to store processed GEO
files. Ignored unless 'processed' flag is
set.[Default: $GEODATA:]
raw:
-x, --split-experiments
Split SRR runs into individual samples. By default,
SRX experiments with multiple SRR Runs will have a
single entry in the annotation table, with each run as
a separate row in the subannotation table. This
setting instead treats each run as a separate sample
-b BAM_FOLDER, --bam-folder BAM_FOLDER
Optional: Specify folder of bam files. Geofetch will
not download sra files when corresponding bam files
already exist. [Default: $SRABAM:]
-f FQ_FOLDER, --fq-folder FQ_FOLDER
Optional: Specify folder of fastq files. Geofetch will
not download sra files when corresponding fastq files
already exist. [Default: $SRAFQ:]
--use-key-subset Use just the keys defined in this module when writing
out metadata.
--add-convert-modifier
Add looper SRA convert modifier to config file.