OpenMS
2.5.0
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Class to write out an OpenSwath OSW SQLite output (PyProphet input). More...
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.h>
Public Member Functions | |
OpenSwathOSWWriter (const String &output_filename, const String &input_filename="inputfile", bool ms1_scores=false, bool sonar=false, bool uis_scores=false) | |
bool | isActive () const |
void | writeHeader () |
Initializes file by generating SQLite tables. More... | |
String | getScore (const Feature &feature, std::string score_name) const |
Prepare scores for SQLite insertion. More... | |
std::vector< String > | getSeparateScore (const Feature &feature, std::string score_name) const |
Prepare concatenated scores for SQLite insertion. More... | |
String | prepareLine (const OpenSwath::LightCompound &, const OpenSwath::LightTransition *, FeatureMap &output, String id) const |
Prepare a single line (feature) for output. More... | |
void | writeLines (const std::vector< String > &to_osw_output) |
Write data to disk. More... | |
Private Attributes | |
String | output_filename_ |
String | input_filename_ |
OpenMS::UInt64 | run_id_ |
bool | doWrite_ |
bool | use_ms1_traces_ |
bool | sonar_ |
bool | enable_uis_scoring_ |
Class to write out an OpenSwath OSW SQLite output (PyProphet input).
The class can take a FeatureMap and create a set of string from it suitable for output to OSW using the prepareLine function. The SQL data is directly linked to the PQP file format described in the TransitionPQPFile class. See also OpenSwathTSVWriter for another output format.
The file format has the following tables:
RUN | ||
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ID | INT | Primary Key (run id) |
FILENAME | TEXT | Original filename associated with the run |
FEATURE | ||
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ID | INT | Primary Key (feature id) |
RUN_ID | INT | Foreign Key (RUN.ID) |
PRECURSOR_ID | INT | Foreign Key (TransitionPQPFile PRECURSOR.ID) |
EXP_RT | REAL | Experimental RT (retention time) of the feature |
NORM_RT | REAL | Normalized RT (retention time) of the feature. The position of the peak group in the normalized retention time space (e.g. fx(RT) where fx describes the transformation fx) |
DELTA_RT | REAL | The difference in retention between expected retention time of the assay and the measured feature retention time (EXP_RT) |
LEFT_WIDTH | REAL | Retention time start of the peak (left width) in seconds |
RIGHT_WIDTH | REAL | Retention time end of the peak (right width) in seconds |
FEATURE_MS1 | ||
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FEATURE_ID | INT | Foreign Key (FEATURE.ID) |
AREA_INTENSITY | REAL | Precursor intensity (area) |
APEX_INTENSITY | REAL | Precursor intensity (apex) |
VAR_... | REAL | Precursor score used in pyProphet |
FEATURE_MS2 | ||
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FEATURE_ID | INT | Foreign Key (FEATURE.ID) |
AREA_INTENSITY | REAL | Summed fragment ion intensity (area) |
TOTAL_AREA_INTENSITY | REAL | Summed total XIC of the whole chromatogram |
APEX_INTENSITY | REAL | Summed fragment ion intensity (apex) |
TOTAL_MI | REAL | Total mutual information (MI) |
VAR_... | REAL | Fragment ion score used in pyProphet |
FEATURE_PRECURSOR | ||
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FEATURE_ID | INT | Foreign Key (FEATURE.ID) |
ISOTOPE | INT | Isotope identifier |
AREA_INTENSITY | REAL | Precursor isotope ion intensity (area) |
APEX_INTENSITY | REAL | Precursor isotope ion intensity (apex) |
FEATURE_TRANSITION | ||
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FEATURE_ID | INT | Foreign Key (FEATURE.ID) |
TRANSITION_ID | INT | Foreign Key (transition identifier) |
AREA_INTENSITY | REAL | Fragment ion intensity (area) |
TOTAL_AREA_INTENSITY | REAL | Total XIC of the whole chromatogram |
APEX_INTENSITY | REAL | Fragment ion intensity (apex) |
TOTAL_MI | REAL | Total mutual information (MI) |
VAR_... | REAL | Fragment ion score used in pyProphet |
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inline |
Prepare scores for SQLite insertion.
Some scores might not be defined, those are reported as NULL
feature | The feature being evaluated |
score_name | The name of the queried score |
Prepare concatenated scores for SQLite insertion.
Some scores might not be defined, those are reported as NULL
feature | The feature being evaluated |
score_name | The name of the queried score |
bool isActive | ( | ) | const |
String prepareLine | ( | const OpenSwath::LightCompound & | , |
const OpenSwath::LightTransition * | , | ||
FeatureMap & | output, | ||
String | id | ||
) | const |
Prepare a single line (feature) for output.
The result can be flushed to disk using writeLines (either line by line or after collecting several lines).
pep | The compound (peptide/metabolite) used for extraction |
transition | The transition used for extraction |
output | The feature map containing all features (each feature will generate one entry in the output) |
id | The transition group identifier (peptide/metabolite id) |
void writeHeader | ( | ) |
Initializes file by generating SQLite tables.
void writeLines | ( | const std::vector< String > & | to_osw_output | ) |
Write data to disk.
Takes a set of pre-prepared data statements from prepareLine and flushes them to disk
to_osw_output | Statements generated by prepareLine |
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