2.3 Post‐Processing: SGSeq Parser - labbces/SpliceScape GitHub Wiki

This is the final stage, executed by the merging_outputs.py script. The primary goal of this step is to create a single, unified SQLite database that consolidates the results from all preceding splicing analyses.

The script first defines the final database structure, creating two interconnected tables: splicing_events and sample_info. It then iterates through each sample and calls the appropriate parser (currently majiq_parser) to populate these tables. The result is a clean, relational, and queryable database containing all splicing information generated by the pipeline.

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Inputs and Outputs

Type	Description
Input	• The main directory containing the MAJIQ voila output files. • A text file listing all SRA accessions that were processed. • The species name.
Output	A single SQLite database file (.db) containing the final, consolidated results.

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Final Database Schema

The script generates the definitive database with the following two tables:

splicing_events Table

This table stores unique information about each splicing event identified across all samples.

Column	Description
event_id	A unique identifier for the specific splicing event.
search_id	A simplified identifier used for linking tables.
gene_name	The name of the gene where the event occurs.
seqid	The chromosome or scaffold ID.
strand	The strand of the gene (+ or -).
event_type	The type of event (e.g., ALTA, EX, IR).
start, end	The start and end coordinates of the event's primary junction.
coord	A simplified coordinate string (seqid:start-end).
full_coord	The full coordinate string of the event, compatible with genome browsers.
species	The name of the species.

sample_info Table

This table stores the quantitative data for each event on a per-sample basis, linking back to the splicing_events table.

Column	Description
event_id	Foreign key linking to the splicing_events table.
de_novo	Indicates if the event was discovered 'de novo' (1) or was from existing annotation (0).
mean_psi_majiq	The Percent Spliced-In (PSI) value for the event as calculated by MAJIQ.
psi_sgseq	The PSI value for the event as calculated by SGSeq (to be integrated).
sra_id	The SRA accession ID of the sample.
majiq, sgseq	Flags (1 or 0) indicating which tool detected this event.
species	The name of the species.

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Script Arguments

Argument	Function	Required
--db	Path to the final SQLite database file that will be created.	Yes
--voila	Path to the parent directory containing the per-sample MAJIQ output folders.	Yes
--spp	The name of the species being processed.	Yes
--srr_list	Path to a text file containing the SRA accessions (one per line) to process.	Yes
--ref-table	Optional. The name of a table in the database (e.g., the metadata table) to link the sra_id to.	No
--ref-column	Optional. The column name in the reference table to link with sra_id. Defaults to sra_id.	No

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Run Example

python3 merging_outputs.py --db "final_splicing_database.db" \```
                           ```--voila "/path/to/MAJIQ_results/voila/" \```
                           ```--spp "Arabidopsis_thaliana" \```
                           ```--srr_list "processed_samples.txt"