/**
* This method is called to execute the action that the StepInstance must perform.
*
* @param stepInstance containing the parameters for executing.
* @param temporaryFileDirectory
* @throws Exception could be anything thrown by the execute method.
*/
@Override
public void execute(StepInstance stepInstance, String temporaryFileDirectory) {
// Retrieve raw results for protein range.
Map<String, RawProtein<PfamHmmer3RawMatch>> rawMatches =
rawMatchDAO.getRawMatchesForProteinIdsInRange(
stepInstance.getBottomProtein(),
stepInstance.getTopProtein(),
getSignatureLibraryRelease());
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("PfamA: Retrieved " + rawMatches.size() + " proteins to post-process.");
int matchCount = 0;
for (final RawProtein rawProtein : rawMatches.values()) {
matchCount += rawProtein.getMatches().size();
}
LOGGER.debug("PfamA: A total of " + matchCount + " raw matches.");
}
// Post process
try {
Map<String, RawProtein<PfamHmmer3RawMatch>> filteredMatches =
getPostProcessor().process(rawMatches);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug(
"PfamA: " + filteredMatches.size() + " proteins passed through post processing.");
int matchCount = 0;
for (final RawProtein rawProtein : filteredMatches.values()) {
matchCount += rawProtein.getMatches().size();
}
LOGGER.debug("PfamA: A total of " + matchCount + " matches PASSED.");
}
filteredMatchDAO.persist(filteredMatches.values());
} catch (IOException e) {
throw new IllegalStateException(
"IOException thrown when attempting to post process filtered matches.", e);
}
}
/**
* @param stepInstance containing the parameters for executing.
* @param temporaryFileDirectory is the relative path in which files are stored.
* @return
*/
@Override
protected List<String> createCommand(StepInstance stepInstance, String temporaryFileDirectory) {
final String fastaFilePathName =
stepInstance.buildFullyQualifiedFilePath(
temporaryFileDirectory, this.getFastaFileNameTemplate());
final String statsFilePathName =
stepInstance.buildFullyQualifiedFilePath(
temporaryFileDirectory, this.getStatsFileNameTemplate());
final String fileNameTblout =
stepInstance.buildFullyQualifiedFilePath(
temporaryFileDirectory, outputFileNameTbloutTemplate);
final String outputFileName =
stepInstance.buildFullyQualifiedFilePath(temporaryFileDirectory, outputFileTemplate);
List<String> command = new ArrayList<String>();
if (this.getFullPathToPython().trim().isEmpty()) {
command.add("python");
} else {
command.add(this.getFullPathToPython());
}
command.add(this.fullPathToPfsearchWrapper);
command.add(fileNameTblout);
command.add(fastaFilePathName);
command.add(statsFilePathName);
command.add(outputFileName);
command.add(this.getModelDir());
command.add(this.getFullPathToPFsearch());
command.addAll(this.getBinarySwitchesAsList());
// command.add(fastaFilePathName);
LOGGER.debug("binary command: " + command.toString());
return command;
}
