homopolymer / bigBlastParser

Parse (very big) NCBI BLAST xml output files (very fast) into an SQLite DB.

bigBlastParser

bigBlastParser is a very fast (SAX-style) NCBI BLAST parser for very large BLAST XML files.

It will parse the BLAST data into a SQLite database, generating three tables query, hit, hsp, that can be queried using standard SQL.

The tables are designed as follows:

    CREATE TABLE query(
            query_id      INTEGER,
            query_num     INTEGER,
            query_def     TEXT,
            query_len     INTEGER,
            PRIMARY KEY (query_id)
            );
    CREATE INDEX Fquery ON query (query_id);

    CREATE TABLE hit(
            query_id      INTEGER,
            hit_id        INTEGER,
            hit_num       INTEGER,
            gene_id       TEXT,
            accession     TEXT,
            definition    TEXT,
            length        INTEGER,
            PRIMARY KEY (hit_id),
            FOREIGN KEY (query_id) REFERENCES query (query_id)
            );
    CREATE INDEX Fhit ON hit (hit_id);
    CREATE INDEX Fhit_hit_query ON hit (query_id, hit_id);
    CREATE INDEX Fhit_query ON hit (query_id);

    CREATE TABLE hsp(
            query_id      INTEGER,
            hit_id        INTEGER,
            hsp_id        INTEGER,
            hsp_num       INTEGER,
            bit_score     FLOAT,
            score         INTEGER,
            evalue        FLOAT,
            query_from    INTEGER,
            query_to      INTEGER,
            hit_from      INTEGER,
            hit_to        INTEGER,
            query_frame   INTEGER,
            hit_frame     INTEGER,
            identity      INTEGER,
            positive      INTEGER,
            gaps          INTEGER,
            align_len     INTEGER,
            qseq          TEXT,
            hseq          TEXT,
            midline       TEXT,
            PRIMARY KEY (hsp_id),
            FOREIGN KEY (hit_id) REFERENCES hit (hit_id)
            FOREIGN KEY (query_id) REFERENCES query (query_id)
            );
    CREATE INDEX Fhsp ON hsp (hsp_id);
    CREATE INDEX Fhsp_hit ON hsp (hit_id);
    CREATE INDEX Fhsp_hit_query ON hsp (query_id, hit_id, hsp_id);
    CREATE INDEX Fhsp_query ON hsp (query_id);

The maximum number of hits parsed per query, and the maximum number of hsps parsed per hit are controlled by command line options.

Install

You will need the Xerces-C++ XML parser and SQLite. On Ubuntu use

apt-get install libxerces-c-dev libsqlite3-dev

then download and build the program:

git clone https://github.com/gschofl/BigBlastParser.git
cd BigBlastParser
make
make clean

Command line usage

Usage

bigBlastParser [options] <blastfile>.xml

-o, --out 	dbName        Output SQLite database (default: <blastfile>.db)
-a, --append              Append data to an existing SQLite Blast DB.
--max_hit	n        	  Maximum number of hits parsed from a query (default: 20);
						  (set -1 to parse all available hits)
--max_hit	n 		      Maximum number of hsps parsed from a hit (default: 20);
						  (set -1 to parse all available hsps)
--reset_at  n 	 		  After <n> queries are parsed, the data is dumped to the
                          database file before parsing is resumed. This helps to
                          keep the memory footprint small (default: 1000)
-h, --help                show help