pysradb

https://saket-choudhary.me/pysradb
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pysradb provides a simple method to programmatically access metadata and download sequencing data...
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### Install pysradb from source

Source: https://saket-choudhary.me/pysradb/_sources/installation

Installs pysradb by cloning the GitHub repository and running the setup script. This method is useful for development or when the latest changes are needed directly from the source.

```console
git clone git://github.com/saketkc/pysradb
```

```console
curl  -OL https://github.com/saketkc/pysradb/tarball/master
```

```console
python setup.py install
```

--------------------------------

### Install pysradb using pip

Source: https://saket-choudhary.me/pysradb/_sources/installation

Installs the latest stable release of pysradb using the pip package manager. This is the recommended installation method. Ensure pip is installed.

```console
pip install pysradb
```

--------------------------------

### Set up virtual environment and install pysradb

Source: https://saket-choudhary.me/pysradb/_sources/contributing

Commands to set up a virtual environment named 'pysradb' and install the project in development mode. This ensures that changes made locally are reflected immediately.

```shell
$ mkvirtualenv pysradb
$ cd pysradb/
$ python setup.py develop
```

--------------------------------

### Install pysradb from source

Source: https://saket-choudhary.me/pysradb/installation

Installs pysradb after downloading or cloning the source code. This command should be run from the root directory of the source code.

```bash
python setup.py install
```

--------------------------------

### Fetch Project Metadata using pysradb CLI

Source: https://saket-choudhary.me/pysradb/index

This snippet shows how to retrieve metadata associated with a specific project accession using the `pysradb metadata` command. It requires the project accession as an argument and outputs a table of metadata. No specific dependencies are mentioned beyond having pysradb installed.

```bash
$ pysradb metadata SRP265425

study_accession     experiment_accession    experiment_title        experiment_desc organism_taxid  organism_name   library_name    library_strategy        library_source  library_selection       library_layout  sample_accession        sample_title    instrument      instrument_model        instrument_model_desc   total_spots     total_size      run_accession   run_total_spots run_total_bases
SRP265425   SRX8434255      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 63-2020-04-22   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745319              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     1311358 83306910        SRR11886735     1311358 109594216
SRP265425   SRX8434254      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 62-2020-04-22   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745320              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     2614109 204278682       SRR11886736     2614109 262305651
SRP265425   SRX8434253      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 61-2020-04-22   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745318              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     2286312 183516004       SRR11886737     2286312 263304134
SRP265425   SRX8434252      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 60-2020-04-22   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745317              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     5202567 507524965       SRR11886738     5202567 781291588
SRP265425   SRX8434251      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 38-2020-04-03   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745315              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     3313960 356104406       SRR11886739     3313960 612430817
SRP265425   SRX8434250      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 37-2020-04-03   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745316              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     5155733 565882351       SRR11886740     5155733 954342917
SRP265425   SRX8434249      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 36-2020-04-03   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745313              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     1324589 175619046       SRR11886741     1324589 216531400
SRP265425   SRX8434248      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 35-2020-04-03   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745314              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     1639851 198973268       SRR11886742     1639851 245466005
SRP265425   SRX8434247      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 68-2020-05-07   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745312              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     3921389 210198580       SRR11886743     3921389 332935558
SRP265425   SRX8434246      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 66-2020-04-22   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745311              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     14295475        2150005008      SRR11886744     14295475        2967829315
SRP265425   SRX8434245      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 65-2020-04-22   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745310              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     5124692 294846140       SRR11886745     5124692 431819462
SRP265425   SRX8434244      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 64-2020-04-22   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745309              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     2986306 205666872       SRR11886746     2986306 275400959
SRP265425   SRX8434243      Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 34-2020-04-03   AMPLICON        VIRAL RNA       RT-PCR  SINGLE  SRS6745308              Ion Torrent S5 XL       Ion Torrent S5 XL       ION_TORRENT     1182690 59471336        SRR11886747     1182690 86350631
```

--------------------------------

### Download pysradb source tarball

Source: https://saket-choudhary.me/pysradb/installation

Downloads the source code of pysradb as a tarball from the master branch on GitHub. This is an alternative to cloning the repository.

```bash
curl  -OL https://github.com/saketkc/pysradb/tarball/master
```

--------------------------------

### Clone pysradb from GitHub

Source: https://saket-choudhary.me/pysradb/installation

Clones the pysradb source code repository from GitHub. This is useful for development or obtaining the latest code directly.

```bash
git clone git://github.com/saketkc/pysradb
```

--------------------------------

### Set up Local Development Environment

Source: https://saket-choudhary.me/pysradb/contributing

These commands set up a virtual environment for local development of pysradb. It involves creating a virtual environment, navigating into the project directory, and installing the project in development mode.

```bash
$ mkvirtualenv pysradb
$ cd pysradb/
$ python setup.py develop

```

--------------------------------

### Create conda environment for pysradb

Source: https://saket-choudhary.me/pysradb/installation

Creates a new conda environment named 'pysradb' with Python 3 and the pysradb package installed. This helps isolate dependencies.

```bash
conda create -c bioconda -n pysradb PYTHON=3 pysradb
```

--------------------------------

### Fetch SRA/EBI Metadata via Console with pysradb

Source: https://saket-choudhary.me/pysradb/_sources/quickstart

This command-line snippet demonstrates how to use the pysradb tool to fetch metadata for a given SRA study accession. It requires the pysradb package to be installed and accessible in the system's PATH.

```bash
$ pysradb metadata SRP265425
```

--------------------------------

### Fetch SRA Metadata via Console with pysradb

Source: https://saket-choudhary.me/pysradb/quickstart

This command-line snippet demonstrates how to use the pysradb tool to retrieve metadata for a specific SRA study accession. It requires the pysradb package to be installed and accessible in the system's PATH.

```bash
$ pysradb metadata SRP265425

```

--------------------------------

### Ultrafast FASTQ Download with aspera-client (Console)

Source: https://saket-choudhary.me/pysradb/_sources/quickstart

This console command leverages aspera-client for ultrafast downloads of FASTQ files, utilizing 8 threads for the specified accession number.

```console
$ pysradb download -t 8 --use_ascp -p SRP002605
```

--------------------------------

### Install pysradb using Conda

Source: https://saket-choudhary.me/pysradb/_sources/installation

Installs pysradb and its dependencies using the conda package manager from the bioconda channel. It's recommended to create a new environment for pysradb to avoid package conflicts.

```bash
conda install -c bioconda pysradb
```

```bash
conda create -c bioconda -n pysradb PYTHON=3 pysradb
```

--------------------------------

### Download Sequenching Data via Piped Metadata (Console)

Source: https://saket-choudhary.me/pysradb/_sources/quickstart

This command demonstrates downloading sequencing data by first fetching metadata for a given accession number and then piping it to the download function in the console.

```bash
$ pysradb metadata SRP276671 --detailed | pysradb download
```

--------------------------------

### Get retmax values for pagination in Python

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/sraweb

Generates a sequence of `retstart` values to paginate through a set of records. It yields starting indices for fetching records in batches of a specified maximum size (`retmax`) until all `n_records` are processed.

```python
def get_retmax(n_records, retmax=500):
    """Get retstart and retmax till n_records are exhausted"""
    for i in range(0, n_records, retmax):
        yield i
```

--------------------------------

### pysradb CLI Help and Basic Usage

Source: https://saket-choudhary.me/pysradb/cmdline

Displays the main help message for the pysradb CLI, showing available commands and global options. This is the entry point for understanding the tool's capabilities.

```bash
$ pysradb
usage: pysradb [-h] [--version] [--citation]
               {metadb,metadata,download,search,gse-to-gsm,gse-to-srp,gsm-to-gse,gsm-to-srp,gsm-to-srr,gsm-to-srs,gsm-to-srx,srp-to-gse,srp-to-srr,srp-to-srs,srp-to-srx,srr-to-gsm,srr-to-srp,srr-to-srs,srr-to-srx,srs-to-gsm,srs-to-srx,srx-to-srp,srx-to-srr,srx-to-srs}
               ...

pysradb: Query NGS metadata and data from NCBI Sequence Read Archive.
Citation: 10.12688/f1000research.18676.1

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --citation            how to cite

subcommands:
  {metadb,metadata,download,search,gse-to-gsm,gse-to-srp,gsm-to-gse,gsm-to-srp,gsm-to-srr,gsm-to-srs,gsm-to-srx,srp-to-gse,srp-to-srr,srp-to-srs,srp-to-srx,srr-to-gsm,srr-to-srp,srr-to-srs,srr-to-srx,srs-to-gsm,srs-to-srx,srx-to-srp,srx-to-srr,srx-to-srs}
    metadata            Fetch metadata for SRA project (SRPnnnn)
    download            Download SRA project (SRPnnnn)
    search              Search SRA/ENA for matching text
    gse-to-gsm          Get GSM for a GSE
    gse-to-srp          Get SRP for a GSE
    gsm-to-gse          Get GSE for a GSM
    gsm-to-srp          Get SRP for a GSM
    gsm-to-srr          Get SRR for a GSM
    gsm-to-srs          Get SRS for a GSM
    gsm-to-srx          Get SRX for a GSM
    srp-to-gse          Get GSE for a SRP
    srp-to-srr          Get SRR for a SRP
    srp-to-srs          Get SRS for a SRP
    srp-to-srx          Get SRX for a SRP
    srr-to-gsm          Get GSM for a SRR
    srr-to-srp          Get SRP for a SRR
    srr-to-srs          Get SRS for a SRR
    srr-to-srx          Get SRX for a SRR
    srs-to-gsm          Get GSM for a SRS
    srs-to-srx          Get SRX for a SRS
    srx-to-srp          Get SRP for a SRX
    srx-to-srr          Get SRR for a SRX
    srx-to-srs          Get SRS for a SRX

```

--------------------------------

### Extract SRP from Splitted String - Python

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/geodb

Extracts the SRP (Sample and Experiment) identifier from the last element of a split string. It uses regular expressions to find patterns starting with 'SRP' and splits the result by '/' to get the final SRP value. Returns None if no match is found or the string is empty.

```python
import re

# Assuming 'splitted' is a list of strings
splitted = [...] # Example: ['some/path/SRP123456/something', 'another/SRP789012']

if len(splitted):
    match = re.findall("SRP.*", splitted[-1])
    if len(match):
        srp = match[0].split("/")[-1]
        # return srp # This line would typically be within a function
        print(srp) # Example usage outside a function
# return None # This line would typically be within a function
```

--------------------------------

### Install pysradb using conda

Source: https://saket-choudhary.me/pysradb/installation

Installs pysradb and its dependencies using conda from the bioconda channel. This method is recommended for managing environments, especially for complex projects.

```bash
conda install -c bioconda pysradb
```

--------------------------------

### Get File Size from URL (pysradb.download)

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/download

Retrieves the file size for a given URL, supporting both FTP and HTTP(S) protocols. For HTTP, it uses a HEAD request to get the 'content-length' header. For FTP, it calls a helper function. It handles potential errors like timeouts or invalid URLs, returning NaN for invalid URLs.

```python
def get_file_size(row, url_col):
    """Get size of file to be downloaded.

    Parameters
    ----------
    row: pd.DataFrame row

    url_col: str
        url_column

    Returns
    -------
    content_length: int
    """
    if row[url_col] is not None:
        url = row[url_col]
    else:
        url = row.download_url
    if url is pd.NA:
        return 0
    if not isinstance(url, str):
        return 0
    if url.startswith("ftp."):
        url = "ftp://" + url

    if url.startswith("ftp://"):
        return _get_ftp_file_size(url)

    try:
        r = requests_3_retries().head(url)
        size = int(r.headers["content-length"])
        r.raise_for_status()
    except requests.exceptions.Timeout:
        sys.exit(f"Connection to {url} has timed out. Please retry.")
    except requests.exceptions.HTTPError:
        print(
            f"The download URL:  {url}  is likely invalid.\n"
            f"Removing {row.run_accession} from the download list\n",
            flush=True,
        )
        return np.NaN
    except KeyError:
        print("Key error for: " + url, flush=True)
        return 0
    return size

```

--------------------------------

### Run linting and tests

Source: https://saket-choudhary.me/pysradb/_sources/contributing

Commands to check code quality using flake8 and run tests using the built-in setup.py test command or py.test. 'tox' is used to test across multiple Python versions.

```shell
$ flake8 pysradb tests
$ python setup.py test or py.test
$ tox
```

--------------------------------

### Download Entire SRA Project using pysradb

Source: https://saket-choudhary.me/pysradb/_sources/python-api-usage

This code snippet shows how to download all data for a specified SRA project. It first fetches the project's metadata and then initiates the download process. For faster downloads, it is recommended to have 'aspera-client' installed. The function takes a pandas DataFrame of metadata and an optional output directory.

```python
from pysradb import SRAweb
db = SRAweb()
df = db.sra_metadata('SRP017942')
db.download(df)
```

--------------------------------

### Get SRP Identifiers from DOI - Python

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/sraweb

This Python function is designed to extract Sequence Read Archive (SRP) identifiers from provided Digital Object Identifiers (DOIs). It first calls `doi_to_identifiers` to get all associated data and then filters the results to return a DataFrame containing only the DOI, PMID, PMC ID, and SRP IDs. This method facilitates the connection between published literature and raw sequencing data.

```python
def doi_to_srp(self, dois):
    """Get SRP identifiers from DOI(s)

    Parameters
    ----------
    dois: list or str
         DOI(s)

    Returns
    -------
    results_df: pandas.DataFrame
               DataFrame with DOIs and SRP identifiers
    """
    full_results = self.doi_to_identifiers(dois)
    return full_results[["doi", "pmid", "pmc_id", "srp_ids"]]
```

--------------------------------

### Download File from URL with Progress

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/utils

Downloads a file from a given URL to a specified location with an optional progress bar. It supports HTTP, HTTPS, and FTP URLs and creates directories if they don't exist. The progress bar uses `tqdm` for visual feedback.

```python
def _get_url(url, download_to, show_progress=True):
    """Download anything at a given url.

    Parameters
    ----------
    url: string
         http/https/ftp url
    download_to: string
                 File location to write the downloaded file to
    show_progress: bool
                   Set to True by default to print progress bar
    """
    desc_file = "Downloading {}".format(url.split("/")[-1])
    mkdir_p(os.path.dirname(download_to))
    if show_progress:
        with TqdmUpTo(
            unit="B", unit_scale=True, unit_divisor=1024, miniters=1, desc=desc_file
        ) as t:
            urllib_request.urlretrieve(
                url, download_to, reporthook=t.update_to, data=None
            )
    else:
        urllib_request.urlretrieve(url, download_to)
```

--------------------------------

### SRAdb Initialization and Verification

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/sradb

This section details the initialization of the SRAdb class, which involves verifying the integrity and schema version of the SRAmetadb.sqlite file.

```APIDOC
## SRAdb Class Initialization

### Description
Initializes the SRAdb object, connecting to a specified SRAmetadb.sqlite file after verifying its validity. The class is designed to interact with SRA metadata.

### Method
`__init__(self, sqlite_file)`

### Parameters
#### Path Parameters
- **sqlite_file** (string) - Required - Path to the unzipped SRAmetadb.sqlite file.

### Request Body
(Not applicable for initialization)

### Request Example
```python
from pysradb.sradb import SRAdb

db = SRAdb('/path/to/SRAmetadb.sqlite')
```

### Response
#### Success Response (Initialization)
- The `SRAdb` object is created and ready for queries.

#### Response Example
(No direct response body for initialization, but the object is returned)

## _verify_srametadb(filepath)

### Description
Internal function to check if the provided SQLite filepath points to a valid SRAmetadb.sqlite file by examining its schema and metadata.

### Method
`_verify_srametadb(filepath)`

### Parameters
#### Path Parameters
- **filepath** (string) - Required - The path to the SQLite database file to verify.

### Request Body
(Not applicable)

### Request Example
```python
# This function is called internally by SRAdb.__init__
# Example of direct call (not typical usage):
from pysradb.sradb import _verify_srametadb
_verify_srametadb('/path/to/SRAmetadb.sqlite')
```

### Response
#### Success Response (Verification)
- If the file is valid, the function completes without error.

#### Response Example
(No explicit return value on success)
```

--------------------------------

### Get SRX for a SRS Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Experiment (SRX) identifier for a given Sequence Read Sample (SRS) accession.

```python
srs_to_srx(_srs_)
```

--------------------------------

### Download Sequencing Data by Accession Number (Console)

Source: https://saket-choudhary.me/pysradb/_sources/quickstart

This command downloads sequencing data from ENA or SRA using a given accession number directly from the console.

```bash
$ pysradb download SRP098789
```

--------------------------------

### Get SRX for a SRR Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Experiment (SRX) identifier for a given Sequence Read Run (SRR) accession.

```python
srr_to_srx(_srr_)
```

--------------------------------

### Get SRS for a SRR Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Sample (SRS) identifier for a given Sequence Read Run (SRR) accession.

```python
srr_to_srs(_srr_)
```

--------------------------------

### Ultrafast FASTQ Download with aspera-client (Python)

Source: https://saket-choudhary.me/pysradb/_sources/quickstart

This Python code snippet configures pysradb to perform ultrafast FASTQ downloads using aspera-client, specifying the accession number, enabling ascp, and setting the number of threads to 8.

```python
from pysradb.sraweb import SRAweb

db = SRAweb()
db.download("SRP098789", use_ascp=True, threads=8)
```

--------------------------------

### Get Plot Objects (Python)

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/search

Provides a getter method to retrieve the plot objects that have been generated. These objects can be used for further manipulation or display of the plots.

```python
def get_plot_objects(self):
    """Get the plot objects for plots generated."""
    return self.plot_objects

```

--------------------------------

### Download Entire Project Metadata and Data

Source: https://saket-choudhary.me/pysradb/cmdline

This command first downloads detailed metadata for a project accession (SRP) and then pipes it to the download command to fetch all associated data. This is a convenient way to acquire an entire SRA project.

```bash
$ pysradb metadata --detailed SRP098789 | pysradb download

```

--------------------------------

### Get SRS for a SRX Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Sample (SRS) identifiers associated with a given Sequence Read Experiment (SRX) accession.

```python
srx_to_srs(_srx_)
```

--------------------------------

### Fetch Detailed SRA Metadata with pysradb

Source: https://saket-choudhary.me/pysradb/index

This command fetches detailed metadata for a given SRA project accession. It includes information such as run accession, study accession, experiment details, organism information, library parameters, instrument details, and URLs for raw sequencing files.

```bash
$ pysradb metadata SRP265425 --detailed
```

--------------------------------

### Get SRR for a SRX Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Run (SRR) identifiers associated with a given Sequence Read Experiment (SRX) accession.

```python
srx_to_srr(_srx_)
```

--------------------------------

### Run Code Linters and Tests

Source: https://saket-choudhary.me/pysradb/contributing

These commands check your code for style compliance using flake8 and run the project's tests using setup.py or py.test. Tox is also used to test across different Python versions.

```bash
$ flake8 pysradb tests
$ python setup.py test or py.test
$ tox

```

--------------------------------

### Get SRP for a SRX Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Archive Project (SRP) identifier for a given Sequence Read Experiment (SRX) accession.

```python
srx_to_srp(_srx_)
```

--------------------------------

### Download Utilities

Source: https://saket-choudhary.me/pysradb/pysradb

Functions for downloading files, checking file sizes, validating MD5 hashes, and formatting numbers.

```APIDOC
## pysradb.download.download_file

### Description
Resumable download function. Expects the server to support byte ranges.

### Method
Not applicable (function)

### Endpoint
Not applicable (function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **url** (string) - Required - URL of the file to download.
- **file_path** (string) - Required - Local file path to store the downloaded file.
- **md5_hash** (string) - Optional - Expected MD5 string of the downloaded file.
- **timeout** (int) - Optional - Seconds to wait before terminating the request (default: 10).
- **block_size** (int) - Optional - Bytes to read in each chunk (default: 1048576).
- **show_progress** (bool) - Optional - Whether to display a progress bar.

### Request Example
```python
pysradb.download.download_file("http://example.com/file.txt", "./local/path/file.txt", md5_hash="abcdef12345")
```

### Response
#### Success Response (200)
N/A (function returns None, but downloads file)

#### Response Example
None
```

```APIDOC
## pysradb.download.get_file_size

### Description
Get the size of a file to be downloaded.

### Method
Not applicable (function)

### Endpoint
Not applicable (function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **row** (pd.DataFrame row) - Required - A row from a pandas DataFrame containing URL information.
- **url_col** (str) - Required - The name of the column in the DataFrame that contains the URL.

### Request Example
```python
# Assuming df is a pandas DataFrame with a 'URL' column
file_size = pysradb.download.get_file_size(df.iloc[0], 'URL')
```

### Response
#### Success Response (200)
- **content_length** (int) - The size of the file in bytes.
```

```APIDOC
## pysradb.download.md5_validate_file

### Description
Check if a file's content matches the expected MD5 hash.

### Method
Not applicable (function)

### Endpoint
Not applicable (function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **file_path** (string) - Required - Path to the file to validate.
- **md5_hash** (string) - Required - The expected MD5 hash of the file.

### Request Example
```python
is_valid = pysradb.download.md5_validate_file("./downloaded_file.txt", "abcdef12345")
```

### Response
#### Success Response (200)
- **valid** (bool) - True if the expected and observed MD5 hashes match, False otherwise.
```

```APIDOC
## pysradb.download.millify

### Description
Convert an integer into a human-readable format (e.g., 1000 to '1K').

### Method
Not applicable (function)

### Endpoint
Not applicable (function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **n** (int) - Required - The integer to format.

### Request Example
```python
formatted_number = pysradb.download.millify(1500000)
# formatted_number will be '1.5M'
```

### Response
#### Success Response (200)
- **millidx** (str) - The human-readable formatted string.
```

--------------------------------

### Clone pysradb repository

Source: https://saket-choudhary.me/pysradb/_sources/contributing

Command to clone the pysradb repository locally. This is the first step in setting up the project for local development.

```shell
$ git clone git@github.com:your_name_here/pysradb.git
```

--------------------------------

### Get SRP for a SRR Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Archive Project (SRP) identifier for a given Sequence Read Run (SRR) accession.

```python
srr_to_srp(_srr_)
```

--------------------------------

### Get Filename from Filepath (Python)

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/utils

Extracts the filename (tail) from a given file path. It handles different path formats and returns the last component of the path.

```python
import ntpath

def path_leaf(path):
    """Get path's tail from a filepath.

    Parameters
    ----------
    path: string
          Filepath

    Returns
    -------
    tail: string
          Filename
    """
    head, tail = ntpath.split(path)
    return tail or ntpath.basename(head)
```

--------------------------------

### Fetch SRA Project Metadata (Basic)

Source: https://saket-choudhary.me/pysradb/cmdline

Retrieves basic metadata for a given SRA project accession (SRPnnnn). This output includes study, experiment, sample, and run accessions, providing a foundational overview of the project's components.

```bash
$ pysradb metadata SRP098789

 study_accession experiment_accession sample_accession run_accession
 SRP098789       SRX2536403           SRS1956353       SRR5227288
 SRP098789       SRX2536404           SRS1956354       SRR5227289
 SRP098789       SRX2536405           SRS1956355       SRR5227290
 SRP098789       SRX2536406           SRS1956356       SRR5227291
 SRP098789       SRX2536407           SRS1956357       SRR5227292
 SRP098789       SRX2536408           SRS1956358       SRR5227293
 SRP098789       SRX2536409           SRS1956359       SRR5227294


```

--------------------------------

### Get GSM for a SRX Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Gene Expression Omnibus (GEO) Sample ID (GSM) for a given Sequence Read Experiment (SRX) accession.

```python
srx_to_gsm(_srx_)
```

--------------------------------

### Search and Show Statistics (Bash and Python)

Source: https://saket-choudhary.me/pysradb/_sources/quickstart

Demonstrates how to search the ENA database for specific organisms and retrieve summary statistics of the results. This can be performed directly from the command line or programmatically using Python. It requires the pysradb library.

```bash
$ pysradb search --db ena --organism "Severe acute respiratory syndrome coronavirus 2" --max 10000 -s
```

```python
from pysradb.search import EnaSearch
instance = EnaSearch(return_max=10000, organism="Severe acute respiratory syndrome coronavirus 2")
instance.search()
instance.show_result_statistics()
```

--------------------------------

### Get GSM for a SRS Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Gene Expression Omnibus (GEO) Sample ID (GSM) for a given Sequence Read Sample (SRS) accession.

```python
srs_to_gsm(_srs_)
```

--------------------------------

### Get GSM for a SRR Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Gene Expression Omnibus (GEO) Sample ID (GSM) for a given Sequence Read Run (SRR) accession.

```python
srr_to_gsm(_srr_)
```

--------------------------------

### Initialize and Open SRAdb Connection (Python)

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/basedb

Initializes the BASEdb class by taking the path to an SRAmetadb.sqlite file and opening a read-only connection to it. It also sets up a database cursor for executing queries. Dependencies include the `sqlite3` module for database interaction.

```Python
import sqlite3
import pandas as pd

class BASEdb(object):
    def __init__(self, sqlite_file):
        """Initialize SRAdb.

        Parameters
        ----------

        sqlite_file: string
                     Path to unzipped SRAmetadb.sqlite file


        """
        self.sqlite_file = sqlite_file
        self.open()
        self.cursor = self.db.cursor()


    def open(self):
        """Open sqlite connection."""
        self.db = sqlite3.connect("file:{}?mode=ro".format(self.sqlite_file), uri=True)
        self.db.text_factory = str

```

--------------------------------

### Get SRX for a SRP Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Experiment (SRX) identifiers associated with a given Sequence Read Archive Project (SRP) accession.

```python
srp_to_srx(_srp_)
```

--------------------------------

### Download Sequencing Data via Piped Metadata (Python)

Source: https://saket-choudhary.me/pysradb/_sources/quickstart

This Python code snippet shows how to download sequencing data by first retrieving detailed metadata for an accession number and then passing the resulting DataFrame to the download function.

```python
from pysradb.sraweb import SRAweb
db = SRAweb()
df = db.sra_metadata('SRP016501', detailed=True)
db.download(df=df)
```

--------------------------------

### Deploy to PyPI

Source: https://saket-choudhary.me/pysradb/contributing

This sequence of commands is used by maintainers to deploy new versions of pysradb to PyPI. It involves committing changes, updating the version using bumpversion, and pushing to GitHub and tags. CI handles the deployment to PyPI if tests pass.

```bash
$ bumpversion patch # possible: major / minor / patch
$ git push
$ git push --tags

```

--------------------------------

### Get SRS for a SRP Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Sample (SRS) identifiers associated with a given Sequence Read Archive Project (SRP) accession.

```python
srp_to_srs(_srp_)
```

--------------------------------

### Get SRR for a SRP Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Sequence Read Run (SRR) identifiers associated with a given Sequence Read Archive Project (SRP) accession.

```python
srp_to_srr(_srp_)
```

--------------------------------

### Select Best Download URL based on Protocol Preference

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/sradb

This method iterates through a list of potential download URLs for a given row of data and selects the most suitable one based on the 'use_ascp' flag. If 'use_ascp' is true, it prioritizes URLs starting with 'fasp' (Aspera). Otherwise, it prioritizes 'http' URLs, followed by 'ftp' URLs. If no suitable URL is found, it returns None.

```python
    def _select_best_url(self, url_list, row, use_ascp):
        if use_ascp:
            for url in url_list:
                if str(row[url]).startswith("fasp"):
                    return row[url]
        else:
            for url in url_list:
                if str(row[url]).startswith("http"):
                    return row[url]
            for url in url_list:
                if str(row[url]).startswith("ftp"):
                    return row[url]
        return None
```

--------------------------------

### Get GSE for a SRP Accession

Source: https://saket-choudhary.me/pysradb/pysradb

Retrieves the Gene Set Enrichment (GSE) identifier associated with a given Sequence Read Archive Project (SRP) accession.

```python
srp_to_gse(_srp_)
```

--------------------------------

### Commit and Push Changes

Source: https://saket-choudhary.me/pysradb/contributing

This sequence of commands stages all changes, commits them with a descriptive message, and pushes the branch to your GitHub repository. Replace 'Your detailed description of your changes.' with a summary of your contributions.

```bash
$ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

```

--------------------------------

### Load Embedding Model (Python)

Source: https://saket-choudhary.me/pysradb/_modules/pysradb/metadata_enrichment

Loads the embedding model based on the specified backend. Supports 'sentence-transformers' and 'fastembed'. Raises ImportError if the required library is not installed and ValueError for unsupported backends.

```python
    def _load_model(self):
        """Load the embedding model."""
        if self.backend == "sentence-transformers":
            try:
                from sentence_transformers import SentenceTransformer

                return SentenceTransformer(self.model_name)
            except ImportError:
                raise ImportError(
                    "sentence-transformers required. Install with: pip install sentence-transformers"
                )
        elif self.backend == "fastembed":
            try:
                from fastembed import TextEmbedding

                return TextEmbedding(model_name=self.model_name)
            except ImportError:
                raise ImportError(
                    "fastembed required. Install with: pip install fastembed"
                )
        else:
            raise ValueError(f"Unsupported backend: {self.backend}")
```

--------------------------------

### Deploying pysradb to PyPI

Source: https://saket-choudhary.me/pysradb/_sources/contributing

Commands for maintainers to deploy a new version of pysradb. It involves committing changes, updating the history, bumping the version, and pushing tags. CI handles the PyPI deployment.

```shell
$ bumpversion patch # possible: major / minor / patch
$ git push
$ git push --tags
```
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