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JAL-2629 fix file format issues preventing hmmsearch, jackhmmer running
[jalview.git]
/
src
/
jalview
/
hmmer
/
JackHMMER.java
diff --git
a/src/jalview/hmmer/JackHMMER.java
b/src/jalview/hmmer/JackHMMER.java
index
16dcebb
..
58b1b75
100644
(file)
--- a/
src/jalview/hmmer/JackHMMER.java
+++ b/
src/jalview/hmmer/JackHMMER.java
@@
-72,13
+72,14
@@
public class JackHMMER extends HmmerCommand
try
{
try
{
- File seqFile = FileUtils.createTempFile("seq", ".fa");
+ File seqFile = FileUtils.createTempFile("seq", ".sto");
File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
".sto");
File searchOutputFile = FileUtils.createTempFile("searchOutput",
".txt");
File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
".sto");
File searchOutputFile = FileUtils.createTempFile("searchOutput",
".txt");
- exportSequence(seq, seqFile.getAbsoluteFile());
+ exportStockholm(new SequenceI[] { seq }, seqFile.getAbsoluteFile(),
+ null, true);
boolean ran = runCommand(searchOutputFile, hitsAlignmentFile,
seqFile);
boolean ran = runCommand(searchOutputFile, hitsAlignmentFile,
seqFile);
@@
-244,11
+245,16
@@
public class JackHMMER extends HmmerCommand
* no external database specified for search, so
* export current alignment as 'database' to search
*/
* no external database specified for search, so
* export current alignment as 'database' to search
*/
- databaseFile = FileUtils.createTempFile("database", ".fa");
+ databaseFile = FileUtils.createTempFile("database", ".sto");
AlignmentI al = af.getViewport().getAlignment();
AlignmentI copy = new Alignment(al);
AlignmentI al = af.getViewport().getAlignment();
AlignmentI copy = new Alignment(al);
+
deleteHmmSequences(copy);
deleteHmmSequences(copy);
- exportFasta(copy, databaseFile);
+
+ // jackhmmer fails if file contains duplicate sequence names
+ renameDuplicates(copy.getSequencesArray());
+
+ exportStockholm(copy.getSequencesArray(), databaseFile, null, true);
}
args.add(getFilePath(seqFile, true));
}
args.add(getFilePath(seqFile, true));