/**
* Ensures an accession from MUSCLE is in a format suitable for phylip. Each accession must be
* unique to 10chars (sigh)
*/
protected String fasta_accession2phylip(String accsn) {
if (accsn.length() > 10) {
return accsn.substring(0, 10);
} else {
StringBuffer tmp = new StringBuffer(accsn);
int n_spaces = 10 - accsn.length();
while (n_spaces-- > 0) {
tmp.append(" ");
}
return tmp.toString();
}
}
/**
* Converts the fasta sequences into phylip format: <number of sequences> <length of aligned
* sequences> <id - exactly ten-space character padded><sequence for id> ...
*
* @param fasta_aligned_sequences
* @return the phylip formatted result
*/
protected String fasta2phylip(String fasta_aligned_sequences) throws IOException {
StringBuffer seq = new StringBuffer();
int count = 0;
int length = 0;
boolean prev = false;
BufferedReader rdr = new BufferedReader(new StringReader(fasta_aligned_sequences));
String line;
String cur_id = null;
StringBuffer tmp = new StringBuffer();
while ((line = rdr.readLine()) != null) {
// System.err.println(cur_id+" "+line);
if (line.startsWith(">")) {
count++;
if (prev) {
seq.append(fasta_accession2phylip(cur_id) + tmp + "\n");
cur_id = line.trim().substring(1);
length = tmp.length();
tmp = new StringBuffer();
} else {
prev = true;
cur_id = line.trim().substring(1);
}
} else {
tmp.append(line.trim());
}
}
// dont forget the last sequence
if (tmp.length() > 0) {
seq.append(fasta_accession2phylip(cur_id) + tmp + "\n");
}
return " " + count + " " + length + "\n" + seq.toString();
}
/** {@inheritDoc} */
@Override
protected BufferedDataTable[] execute(
final BufferedDataTable[] inData, final ExecutionContext exec) throws Exception {
if (m_email.equals(DEFAULT_EMAIL)) {
throw new Exception(
"You must set a valid E-Mail for EBI to contact you in the event of problems with the service!");
}
int n_rows = inData[0].getRowCount();
int seq_idx =
inData[0].getSpec().findColumnIndex(((SettingsModelString) m_seq_col).getStringValue());
int accsn_idx =
inData[0].getSpec().findColumnIndex(((SettingsModelString) m_accsn_col).getStringValue());
if (seq_idx < 0 || accsn_idx < 0) {
throw new Exception("Cannot find columns... valid data?");
}
int done = 0;
// create the output columns (raw format for use with R)
DataTableSpec outputSpec = new DataTableSpec(inData[0].getDataTableSpec(), make_output_spec());
BufferedDataContainer container = exec.createDataContainer(outputSpec, false, 0);
// instantiate MUSCLE client
MuscleClient cli = new MuscleClient();
// each row is a separate MUSCLE job, the sequences are in one collection cell, the accessions
// (IDs) in the other
RowIterator it = inData[0].iterator();
while (it.hasNext()) {
DataRow r = it.next();
ListCell seqs = (ListCell) r.getCell(seq_idx);
ListCell accsns = (ListCell) r.getCell(accsn_idx);
if (seqs.size() != accsns.size()) {
throw new Exception(
"Every sequence must have a corresponding accession: error at row "
+ r.getKey().getString());
}
if (seqs.size() < 1) {
throw new Exception("Cannot MUSCLE zero sequences: error at row " + r.getKey().getString());
}
if (seqs.size() > 1000) {
throw new Exception("Too many sequences in row " + r.getKey().getString());
}
// dummy a fake "FASTA" file (in memory) and then submit that to MUSCLE@EBI along with other
// necessary parameters
StringBuffer seq_as_fasta = new StringBuffer();
for (int i = 0; i < seqs.size(); i++) {
seq_as_fasta.append(">");
seq_as_fasta.append(accsns.get(i).toString());
seq_as_fasta.append("\n");
seq_as_fasta.append(seqs.get(i).toString());
seq_as_fasta.append("\n");
}
// System.err.println(seq_as_fasta);
// lodge the muscle job and store the results in the output table
InputParameters ip = new InputParameters();
ip.setSequence(seq_as_fasta.toString());
// start the job
String jobId = cli.runApp(m_email.getStringValue(), r.getKey().getString(), ip);
exec.checkCanceled();
exec.setProgress(((double) done) / n_rows, "Executing " + jobId);
Thread.sleep(20 * 1000); // 20 seconds
waitForCompletion(cli, exec, jobId);
done++;
// process results and add them into the table...
// 1. fasta alignment data
byte[] bytes = cli.getSrvProxy().getResult(jobId, "aln-fasta", null);
DataCell[] cells = new DataCell[3];
cells[0] = new StringCell(jobId);
// compute the base64 encoded phylip aligned sequences suitable for use by R's phangorn
// package
String fasta = new String(bytes);
String ret = fasta2phylip(fasta);
// it must be encoded (I chose base64) as it is common to both Java and R and it must be
// encoded due to containing multiple lines, which confuses the CSV passed between KNIME and R
String rk = r.getKey().getString();
DataCell mac = AlignmentCellFactory.createCell(fasta, AlignmentType.AL_AA);
if (mac instanceof MultiAlignmentCell) m_muscle_map.put(rk, (MultiAlignmentCell) mac);
cells[1] = mac;
bytes = cli.getSrvProxy().getResult(jobId, "out", null);
cells[2] = new StringCell("<html><pre>" + new String(bytes));
container.addRowToTable(new JoinedRow(r, new DefaultRow(r.getKey(), cells)));
}
container.close();
BufferedDataTable out = container.getTable();
return new BufferedDataTable[] {out};
}