Package ubic.gemma.core.analysis.sequence

Class RepeatScan

java.lang.Object

ubic.gemma.core.analysis.sequence.RepeatScan

public class RepeatScan
extends Object

Scan sequences for repeats using RepeatMasker.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
RepeatScan(String repeatMaskerExe)

Method Summary

Modifier and Type	Method	Description
Collection<BioSequence>	processRepeatMaskerOutput(Collection<BioSequence> sequences, Path outputSequencePath)
Collection<BioSequence>	repeatScan(Collection<BioSequence> sequences)	Run RepeatMasker on the sequences.

Methods inherited from class java.lang.Object

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

Constructor Details

RepeatScan

public RepeatScan(String repeatMaskerExe)

Method Details

processRepeatMaskerOutput

public Collection<BioSequence> processRepeatMaskerOutput(Collection<BioSequence> sequences,
 Path outputSequencePath)

Parameters:

sequences - sequences

outputSequencePath - in FASTA format

Returns:

Sequences which were updated.

repeatScan

public Collection<BioSequence> repeatScan(Collection<BioSequence> sequences)

Run RepeatMasker on the sequences. The sequence will be updated with the masked (lower-case) sequences and the fraction of masked bases will be filled in.

Parameters:

sequences - sequences

Returns:

sequences that had repeats.