org.jbei.ice.lib.search.blast

Class BlastPlus

java.lang.Object

org.jbei.ice.lib.search.blast.BlastPlus

public class BlastPlus
extends Object

Enables (command line) interaction with BLAST+

Current usage is for blast searches and auto-annotation support

Author:

Hector Plahar

Constructor Summary

Constructors

Constructor and Description
BlastPlus()

Method Summary

Modifier and Type	Method and Description
static IndexBuildStatus	getStatus()
static List<DNAFeature>	processFeaturesBlastOutput(String blastOutput) Process the output of the blast run for features into a list of feature objects Expected format for the output (per line) is feature_id, label, type, qstart, qend, sstart, send, sstrand Therefore line[0] is feature_id, line[1] is label etc Since we are only interested in features that have a full match (covers entire feature) some matches are manually eliminated.
static void	rebuildDatabase(boolean force) Re-builds the blast database, using a lock file to prevent concurrent rebuilds.
static void	rebuildFeaturesBlastDatabase(String featureFolder)
static HashMap<String,SearchResult>	runBlast(BlastQuery query) Run a blast query using the following output format options stitle - subject title qstart - query match start index qend - query match end index sstart - subject match start index send sstrand evalue bitscore length - alignment length nident - number of identical matches
static List<Bl2SeqResult>	runBlast2Seq(String query, String subject) Run the bl2seq program on multiple subjects.
static List<DNAFeature>	runCheckFeatures(BlastQuery query) Run a blast query against the sequence features blast database.
static void	scheduleBlastIndexRebuildTask(boolean force) Schedule task to rebuild the blast index

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BlastPlus

public BlastPlus()

Method Detail

runBlast

public static HashMap<String,SearchResult> runBlast(BlastQuery query)
                                             throws BlastException

Run a blast query using the following output format options

• stitle - subject title
• qstart - query match start index
• qend - query match end index
• sstart - subject match start index
• send
• sstrand
• evalue
• bitscore
• length - alignment length
• nident - number of identical matches

Parameters:

query - wrapper around blast query

Returns:

map of unique entry identifier (whose sequence was a subject) to the search result hit details

Throws:

BlastException

runCheckFeatures

public static List<DNAFeature> runCheckFeatures(BlastQuery query)
                                         throws BlastException

Run a blast query against the sequence features blast database.

Parameters:

query - wrapper around sequence to blast

Returns:

list of DNA features that match the query according to the parameters

Throws:

BlastException - on null result or exception processing the result

processFeaturesBlastOutput

public static List<DNAFeature> processFeaturesBlastOutput(String blastOutput)

Process the output of the blast run for features into a list of feature objects
Expected format for the output (per line) is feature_id, label, type, qstart, qend, sstart, send, sstrand Therefore line[0] is feature_id, line[1] is label etc
Since we are only interested in features that have a full match (covers entire feature) some matches are manually eliminated. The results returned by blast can cover only a subset of the sequence. e.g. given query = 'ATGC' and feature1 = 'ATG' and feature2 = 'TATGT', the query will return 1,3,1,3 and 1,3,2,4.

Parameters:

blastOutput - blast program output

Returns:

list of feature objects resulting from processing the blast output

rebuildFeaturesBlastDatabase

public static void rebuildFeaturesBlastDatabase(String featureFolder)
                                         throws IOException

Throws:

IOException

rebuildDatabase

public static void rebuildDatabase(boolean force)
                            throws BlastException

Re-builds the blast database, using a lock file to prevent concurrent rebuilds. The lock file has a "life-span" of 1 day after which it is deleted.

Also, a rebuild can be forced even if a lock file exists which is less than a day old

Parameters:

force - set to true to force a rebuild. Use with caution

Throws:

BlastException

runBlast2Seq

public static List<Bl2SeqResult> runBlast2Seq(String query,
                                              String subject)
                                       throws BlastException

Run the bl2seq program on multiple subjects.

This method requires disk space write temporary files. It tries to clean up after itself.

Parameters:

query - reference sequence.

subject - query sequence.

Returns:

List of output string from bl2seq program.

Throws:

BlastException

scheduleBlastIndexRebuildTask

public static void scheduleBlastIndexRebuildTask(boolean force)

Schedule task to rebuild the blast index

getStatus

public static IndexBuildStatus getStatus()