/** {@inheritDoc} */
@Override
public String get_syntax() {
StringBuffer ReturnString =
new StringBuffer(
"Module to srf2fastq: Generate a fastq compatible with a particular aligner, directly from a SRF"
+ System.getProperty("line.separator")
+ System.getProperty("line.separator"));
// Parse relevant parameters
ReturnString.append(
"Example: srf2fastq -a bfast -s illumina [-e 2] [-n 2] -i input.srf [-o outputPrefix]");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append("Required Parameters:");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(
"\t-i, --input {String} Specifies the SRF file that will be read in to produce a fastq");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append("\t-b, --bin {String} Specifies the srf2fastq binary");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(
"\t-f, --filter {String} Specifies that the quality filter for srf2fastq should be used");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(
"\t-s, --sequencer {String} See below for currently supported sequencers");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(
"\t-a, --aligner {String} See below for currently supported aligners");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append("Optional Parameters:");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(
"\t-e, --ends {int} Specifies the number of ends in this SRF. Default: 1 (single-end)");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(
"\t-n, --num-output-files {int} Specifies the number of output files to split normal output files into. Default: 1");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(
"\t-o, --output-prefix {String} Specifies the name to be prepend to each output file. Default: use the name of the input file, truncating '.srf'");
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append("Supported Aligners (for -a argument):");
ReturnString.append(System.getProperty("line.separator"));
for (int i = 0; i < SRF2Fastq.getAligners().length; i++) {
ReturnString.append("\t" + SRF2Fastq.getAligners(i));
ReturnString.append(System.getProperty("line.separator"));
}
ReturnString.append(System.getProperty("line.separator"));
ReturnString.append("Supported Sequencers (for -s argument):");
ReturnString.append(System.getProperty("line.separator"));
for (int i = 0; i < SRF2Fastq.getSequencers().length; i++) {
ReturnString.append("\t" + SRF2Fastq.getSequencers(i));
ReturnString.append(System.getProperty("line.separator"));
}
// Return as string
return ReturnString.toString();
}
/** {@inheritDoc} */
@Override
public ReturnValue do_verify_parameters() {
// Aligner: Look at each supported method to make sure there is a match
boolean valid = false;
for (int j = 0; j < SRF2Fastq.getAligners().length; j++) {
if (aligner != null && aligner.compareTo(SRF2Fastq.getAligners(j).toLowerCase()) == 0) {
valid = true;
break;
}
}
if (!valid)
return new ReturnValue(
null,
"srf2fastq requires a valid -a or --aligner argument, followed by a supported aligner\n\n"
+ get_syntax(),
1);
// Sequencer: make sure a valid sequencer was specified
valid = false;
for (int j = 0; j < SRF2Fastq.getSequencers().length; j++) {
if (sequencer != null && sequencer.compareTo(SRF2Fastq.getSequencers(j).toLowerCase()) == 0) {
valid = true;
break;
}
}
if (!valid)
return new ReturnValue(
null,
"srf2fastq requires a valid -s or --sequencer argument, followed by a supported sequencer\n\n"
+ sequencer
+ " \n\n"
+ get_syntax(),
1);
// ends and numout must be greater than zero
if (ends <= 0 || numOut <= 0) {
return new ReturnValue(
null,
"When specifying -e or -n, they must be followed by an integer\n\n" + get_syntax(),
1);
}
// Input
if (input == null || !input.endsWith(".srf")) {
return new ReturnValue(
null,
"srf2fastq requires a -i or --input file which is a .srf file\n\n" + get_syntax(),
1);
}
if (FileTools.fileExistsAndExecutable(new File(srf2FastqPath)).getExitStatus()
!= ReturnValue.SUCCESS) {
return new ReturnValue(
null,
"srf2fastq requires a -b or --bin file which is the srf2fastq executable\n\n"
+ get_syntax(),
1);
}
// Return object
return new ReturnValue();
}