Scripts

🟡 get_metadata.py

The Python script get_metadata.py is used to retrieve sequence metadata from the NCBI's SRA (Sequence Read Archive) database and store it in a SQLite database. It allows specifying search filters such as species and library layout (PAIRED or SINGLE) and can export lists of SRA identifiers to text files.

• Requirements:

Category	Requirements
Python	Python 3
Standard Libraries	argparse, time, sqlite3, xml.etree.ElementTree, datetime, os
External Libraries	requests, beautifulsoup4, biopython
Internet Connection	Required to access the NCBI API and Google Scholar
Valid Email & API Key	Necessary to use the NCBI Entrez API (--email and --api_key)

• Arguments:

Argument	Function	Required	Example
--mode	Sets the mode: "all" (for species search) or "srr" (for SRR list)	True	--mode all
-e, --email	Specifies the user email for NCBI Entrez API	True	-e [email protected]
-a, --api_key	Specifies the NCBI API key	True	-a ABCD1234...
--database	SQLite3 database file	True	--database metadata.db
-sp	Species name (required for mode "all")	Cond.	-sp Setaria viridis
-ll	Library layout: SINGLE or PAIRED (required for mode "all")	Cond.	-ll PAIRED
--srr_file	File with SRR accessions (required for mode "srr")	Cond.	--srr_file srr_ids.txt
--max_n_ids	Maximum number of identifiers to return	False	--max_n_ids 1000
--verbose	Enables verbose output	False	--verbose
--keep_unavailable	Keep unavailable datasets in the database	False	--keep_unavailable True
--summary	Displays summary statistics	False	--summary
--srr_list_out	File to export list of filtered SRA accessions	False	--srr_list_out sra_accessions.txt
--srr_list_out_with_pmid	File to export list with associated PMIDs	False	--srr_list_out_with_pmid sra_accessions_with_pmid.txt
-v, --version	Displays the script version	False	-v

ℹ️ Note: If --mode all is used, both -sp and -ll must be provided.
If --mode srr is used, --srr_file must be provided.

• Run example:

python3 get_metadata.py --mode all -e [email protected] -a YOUR_API_KEY -sp "Setaria italica" -ll PAIRED --database metadata.db --verbose --max_n_ids 500

Errors

NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2acd3c2b37f0>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))

🟢 metadata_plots.R

metadata_plots.R

• Requirements:

Category	Requirements
Packages	ggplot2

• Output:

ING	PORT

---

🟢 get_metadata_PacBio.py

The Python script get_metadata_PacBio.py is used to retrieve sequence metadata from the NCBI's SRA (Sequence Read Archive) database and store it in a SQLite database. It allows specifying search filters such as species and library layout (PAIRED or SINGLE) and can export lists of SRA identifiers to text files. This script was modified to retrieve only PacBio data.

• Requirements:

Category	Requirements
Python	Python 3
Standard Libraries	argparse, time, sqlite3, xml.etree.ElementTree, datetime, os
External Libraries	requests, beautifulsoup4, biopython
Internet Connection	Required to access the NCBI API and Google Scholar
Valid Email	Necessary to use the NCBI Entrez API

• Arguments:

Argument	Function	Required	Example
-v, --version	Displays the script version	False	-v
--verbose	Enables verbose output	False	--verbose
--summary	Displays summary statistics	False	--summary
-e, --email	Specifies the user email	True	-e [email protected]
-sp	Specifies the species name	True	-sp Setaria viridis
-ll	Specifies the library layout (SINGLE or PAIRED)	False	-ll PAIRED
--database	Specifies the SQLite3 database file	True	--database database.db
--max_n_ids	Sets the maximum number of identifiers to return	False	--max_n_ids 1000
--srr_list_out	Outputs the list of SRA accessions filtered by species and layout	False	--srr_list_out sra_accessions.txt
--srr_list_out_with_pmid	Outputs the list of SRA accessions with associated PMIDs	False	--srr_list_out_with_pmid sra_accessions_with_pmid.txt

• Run example:

python3 "/home/LandscapeSplicingGrasses/SplicingLandscapeGrasses/metadata/get_metadata_PacBio.py" -e [email protected] -sp "Setaria italica" --database database.db --verbose --max_n_ids 100000

Errors

🟢 metadata_plots_PacBio.R

metadata_plots_PacBio.R

• Requirements:

Category	Requirements
Packages	ggplot2

• Output:

ING	PORT