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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,16 @@ | ||
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| TEMPLATE = app | ||
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| QT -= gui | ||
| QT += sql | ||
| CONFIG += console | ||
| CONFIG -= app_bundle | ||
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| SOURCES += main.cpp | ||
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| include("../app_cli.pri") | ||
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| #include cppNGS library | ||
| INCLUDEPATH += $$PWD/../cppNGSD | ||
| LIBS += -L$$PWD/../bin -lcppNGSD |
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| #include "ToolBase.h" | ||
| #include "NGSD.h" | ||
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| class ConcreteTool | ||
| : public ToolBase | ||
| { | ||
| Q_OBJECT | ||
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| public: | ||
| ConcreteTool(int& argc, char *argv[]) | ||
| : ToolBase(argc, argv) | ||
| { | ||
| } | ||
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| virtual void setup() | ||
| { | ||
| setDescription("Lists all processed samples from the NGSD of the same patient/sample to a given processed sample."); | ||
| setExtendedDescription(QStringList() << "Does not contain the provided process sample itself"); | ||
| addString("ps", "Processd sample name.", false); | ||
| //optional | ||
| addOutfile("out", "Output TSV file. If unset, writes to STDOUT.", true); | ||
| addString("sample_type", "Type(s) of samples (can be a comma-separated list).", true, ""); | ||
| addString("system_type", "Type(s) of processing system (can be a comma-separated list).", true, ""); | ||
| addString("system", "Processing system (short) name(s) (can be a comma-separated list).", true, ""); | ||
| addEnum("mode", "Type of relation (either only same-sample or same-patient (includes same-sample)", true, QStringList() << "SAME_SAMPLE" << "SAME_PATIENT", "SAME_PATIENT"); | ||
| addFlag("test", "Uses the test database instead of on the production database."); | ||
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| changeLog(2023, 11, 15, "initial commit"); | ||
| } | ||
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| virtual void main() | ||
| { | ||
| //init | ||
| NGSD db(getFlag("test")); | ||
| QSharedPointer<QFile> output = Helper::openFileForWriting(getOutfile("out"), true); | ||
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| QString ps_name = getString("ps").trimmed(); | ||
| int provided_ps_id = db.processedSampleId(ps_name).toInt(); | ||
| int provided_s_id = db.sampleId(ps_name).toInt(); | ||
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| //get filter parameter | ||
| QSet<QString> filter_sample_types = getString("sample_type").split(',').toSet(); | ||
| filter_sample_types.remove(""); | ||
| QSet<QString> filter_system_types = getString("system_type").split(',').toSet(); | ||
| filter_system_types.remove(""); | ||
| QSet<QString> filter_systems = getString("system").split(',').toSet(); | ||
| filter_systems.remove(""); | ||
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| //validate filter parameters | ||
| QStringList valid_sample_types = db.getEnum("sample", "sample_type"); | ||
| foreach (const QString& sample_type, filter_sample_types) | ||
| { | ||
| if (!valid_sample_types.contains(sample_type)) THROW(ArgumentException, "Invalid sample type '" + sample_type + "' provided!\n Valid sample types are: " + valid_sample_types.join(",")); | ||
| } | ||
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| QStringList valid_system_types = db.getEnum("processing_system", "type"); | ||
| foreach (const QString& system_type, filter_system_types) | ||
| { | ||
| if (!valid_system_types.contains(system_type)) THROW(ArgumentException, "Invalid processing system type '" + system_type + "' provided!\n Valid system types are: " + valid_system_types.join(",")); | ||
| } | ||
| QStringList valid_system_names = db.getValues("SELECT name_short FROM processing_system"); | ||
| foreach (const QString& system_name, filter_systems) | ||
| { | ||
| if (!valid_system_names.contains(system_name)) THROW(ArgumentException, "Invalid processing system (short) name '" + system_name + "' provided!"); | ||
| } | ||
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| //get same samples | ||
| SameSampleMode mode = (getEnum("mode")=="SAME_PATIENT") ? SameSampleMode::SAME_PATIENT : SameSampleMode::SAME_SAMPLE; | ||
| QSet<int> same_samples = db.sameSamples(provided_s_id, mode); | ||
| // add provided sample id itself to report different processings | ||
| same_samples.insert(provided_s_id); | ||
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| //get processed samples | ||
| QStringList ps_table; | ||
| foreach (int s_id, same_samples) | ||
| { | ||
| SampleData s_data = db.getSampleData(QString::number(s_id)); | ||
| QList<int> ps_ids = db.getValuesInt("SELECT id FROM processed_sample WHERE sample_id=:0", QString::number(s_id)); | ||
| foreach (int ps_id, ps_ids) | ||
| { | ||
| //skip sample itself: | ||
| if (ps_id == provided_ps_id) continue; | ||
| ProcessedSampleData ps_data = db.getProcessedSampleData(QString::number(ps_id)); | ||
| QDate run_start_date = db.getValue("SELECT start_date FROM sequencing_run WHERE name=:0", false, ps_data.run_name).toDate(); | ||
| QString sys_name_short = db.getValue("SELECT name_short FROM processing_system WHERE name_manufacturer=:0", false, ps_data.processing_system).toString(); | ||
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| //apply filter | ||
| if (!filter_sample_types.isEmpty() && !filter_sample_types.contains(s_data.type)) continue; | ||
| if (!filter_system_types.isEmpty() && !filter_system_types.contains(ps_data.processing_system_type)) continue; | ||
| if (!filter_systems.isEmpty() && !filter_systems.contains(sys_name_short)) continue; | ||
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| QStringList line; | ||
| line << ps_data.name; | ||
| line << s_data.type; | ||
| line << sys_name_short; | ||
| line << ps_data.processing_system_type; | ||
| line << ps_data.processing_system; | ||
| line << ps_data.run_name; | ||
| line << run_start_date.toString("dd.MM.yyyy"); | ||
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| ps_table << line.join("\t"); | ||
| } | ||
| } | ||
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| QStringList header_line; | ||
| header_line << "#processed_sample"; | ||
| header_line << "sample_type"; | ||
| header_line << "processing_system_type"; | ||
| header_line << "processing_system_name"; | ||
| header_line << "processing_system_name_short"; | ||
| header_line << "run_id"; | ||
| header_line << "run_date"; | ||
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| //sort by processed sample name | ||
| std::sort(ps_table.begin(), ps_table.end()); | ||
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| //write to output file | ||
| output->write(header_line.join("\t").toUtf8() + '\n'); | ||
| output->write(ps_table.join("\n").toUtf8()); | ||
| output->flush(); | ||
| output->close(); | ||
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| } | ||
| }; | ||
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| #include "main.moc" | ||
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| int main(int argc, char *argv[]) | ||
| { | ||
| ConcreteTool tool(argc, argv); | ||
| return tool.execute(); | ||
| } |
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