| Name | miSRA JSON |
| Version |
0.0.3
JSON |
| download |
| home_page | |
| Summary | A command-line interface to the miSRA API. It allow to remotely query over 90,000 miRNA-seq samples from the Sequence Read Archive |
| upload_time | 2023-07-13 10:31:50 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.7.0 |
| license | |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
requests
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# miSRA
a command line tool to remotely query over 90,000 miRNA-seq samples from the Sequence Read Archive.
For more info, please visit the [GitHub repository](https://github.com/bioinfoUGR/miSRA).
## Dependencies
miSRA requires Python >= 3.7 and the python package *requests* (automatically installed by *pip*)
## How to install
### (*optional but recommended*) Create a virtual environment and activate it
python3 -m venv env
source env/bin/activate
### Install with *pip* (recommended)
pip3 install miSRA
# to test that it worked
miSRA --help
## Run miSRA:
miSRA --config your_config.json
An example [*config.json*](https://github.com/bioinfoUGR/miSRA/tree/master/src/example_configs/miSRA_example_config.json) could include the following parameters (for a detailed explanation of the different query modes, [see **miSRA modes** ](##miSRA-modes)):
{
"mode":"mirna", # There are different modes to query miSRA (mirna, lib and spike). The mode mirna performs alignments to miRNA annotations using sRNAbench
# mirna mode requires 2 miRNA annotation files, one for mature miRNAs and one for hairpins
"mature":"mature_hsa.fa", # path to mature miRNA annotations in fasta format
"hairpin":"hairpin_hsa.fa", # path to hairpin miRNA annotations in fasta format
# you can specify which samples you want to profile either by specifying comma-separated SRA study or experiment accessions
"studies":"SRP225193", # profile all samples from this study
# "experiments":"SRX2349199,SRX2349197,SRX546025,SRX546026", # this would include these experiments
"localOut":"RNAatlas", # local folder where the results will be downloaded to
"mm": "1", # number of mismatches (optional)
"alignType":"v" # bowtie alignment type (optional)
}
One could also download information about the database content. The following command will generate a file in the
current working directory including the number of available samples and studies per species.
miSRA --db-stat
To obtain all samples and studies available for a specific species, you can do:
miSRA --taxonID TAXON_ID
## Where TAXON_ID is NCBI's taxonID. For instance, for human:
miSRA --taxonID 9606
## miSRA modes:
There are 3 main modes to query samples in miSRA:
* **miRNA**: mature and hairpin miRNA sequences are used for profiling
* **library**: long reference sequences are used for profiling and mappings of reads to these sequences will be reported
* **spike**: short reference sequences are provided and only exact matches will be reported
For more info, please visit the [GitHub repository](https://github.com/bioinfoUGR/miSRA) or the tool [manual](https://github.com/bioinfoUGR/miSRA/blob/main/manual.pdf).
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