Python scripts for various manipulation and downloading for genomics.
This python script requires the python package pysradb as a depencency.
I suggest creating a conda environment to install pysradb with this command:
conda create -c bioconda -n pysradb PYTHON=3.10 pysradb
conda activate pysradb
Once the conda environment is set up, you should be ready to run the script! The script pulls from metadata from the NCBI SRA Database from user-given SRA Accessions.
usage: extract_sra_metadata.py [-i INPUT_FILE] [-q QUERIES [QUERIES ...]] [-o OUTPUT] [-h] [-s INPUT_STRING [INPUT_STRING ...]] [--display-all-fields] Extract metadata from SRA Accessions and write to a text file. Required: -i INPUT_FILE List of SRA Accessions to extract metadata info from. -q QUERIES [QUERIES ...] Metadata query or queries of interest. Provide one or two queries. -o OUTPUT Output text file for SRA metadata of interest. Optional: -h, --help show this help message and exit -s INPUT_STRING [INPUT_STRING ...] SRA Accessions as a string. --display-all-fields Display all fields present in the generated JSON file.
The script will take and either a text file with a list of SRA Accessions -i or an SRA Accession or multiple SRA Accessions as a string using -s, with a space separating each SRA Accession.
Here is an example of running the extract_sra_metadata.py script with a list of SRA Accessions as a text file and wanting the instrument and library layout (ex., PAIRED or SINGLE) metadata from the SRA Accessions listed in the text file and outputed in a text file with the name of your choosing:
python extract_sra_metadata.py -i sra_ids.txt -q instrument library_layout -o sra_meta.txt
It will then proceed to print out the information as well as save it to a tab-deliminted text file, such as this:
SRR Accession instrument library_layout
SRR11097771 NextSeq 500 PAIRED
SRR11097772 NextSeq 500 PAIRED
SRR11097773 NextSeq 500 PAIRED
SRR11097774 NextSeq 500 PAIRED
If you are only interested in extracting metadata from one sample, you can use the -s option to only specificy that SRA Accession, as follows:
python extract_sra_metadata.py -s SRR11097771 -q instrument library_layout -o sra_meta.txt
The -s option will also accept more than one SRA Accession, with a space between each one, such as:
python extract_sra_metadata.py -s SRR11097771 SRR11097772 -q instrument library_layout -o sra_meta.txt
Any questions feel free to contact me!