Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ADD] FileConverter FeatureXML to OMS #17

Open
wants to merge 4 commits into
base: idfile-integration
Choose a base branch
from
+37 −20
Open

[ADD] FileConverter FeatureXML to OMS #17

Changes from 1 commit
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
fefe193
add oms to fileconverter
oliveralka Aug 31, 2021
1128150
[FIX]
oliveralka Sep 3, 2021
6a6e611
add fxml export
oliveralka Sep 13, 2021
d40720f
Use qint instead uf quint
oliveralka Oct 4, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 17 additions & 2 deletions src/topp/FileConverter.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,13 +48,17 @@
#include <OpenMS/FORMAT/IBSpectraFile.h>
#include <OpenMS/FORMAT/SqMassFile.h>
#include <OpenMS/FORMAT/CachedMzML.h>
#include <OpenMS/FORMAT/OMSFile.h>
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/KERNEL/ConversionHelper.h>
#include <OpenMS/KERNEL/ChromatogramTools.h>

#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataCachedConsumer.h>
#include <OpenMS/METADATA/ID/IdentificationDataConverter.h>




using namespace OpenMS;
Expand Down Expand Up @@ -125,6 +129,7 @@ using namespace std;
@ref OpenMS::KroenikFile "kroenik"
@ref OpenMS::EDTAFile "edta"
@ref OpenMS::SqMassFile "sqmass"
@ref OpenMS::OMSFile "oms"

@note See @ref TOPP_IDFileConverter for similar functionality for protein/peptide identification file formats.

Expand Down Expand Up @@ -338,7 +343,7 @@ class TOPPFileConverter :
String method("none,ensure,reassign");
setValidStrings_("UID_postprocessing", ListUtils::create<String>(method));

vector<String> output_formats = {"mzML", "mzXML", "cachedMzML", "mgf", "featureXML", "consensusXML", "edta", "mzData", "dta2d", "csv", "sqmass"};
vector<String> output_formats = {"mzML", "mzXML", "cachedMzML", "mgf", "featureXML", "consensusXML", "edta", "mzData", "dta2d", "csv", "sqmass","oms"};
registerOutputFile_("out", "<file>", "", "Output file");
setValidFormats_("out", output_formats);
registerStringOption_("out_type", "<type>", "", "Output file type -- default: determined from file extension or content\nNote: that not all conversion paths work or make sense.", false, true);
Expand Down Expand Up @@ -504,7 +509,8 @@ class TOPPFileConverter :
fh.loadFeatures(in, fm, in_type);
fm.sortByPosition();
if ((out_type != FileTypes::FEATUREXML) &&
(out_type != FileTypes::CONSENSUSXML))
(out_type != FileTypes::CONSENSUSXML) &&
(out_type != FileTypes::OMS))
{
// You will lose information and waste memory. Enough reasons to issue a warning!
writeLog_("Warning: Converting features to peaks. You will lose information! Mass traces are added, if present as 'num_of_masstraces' and 'masstrace_intensity' (X>=0) meta values.");
Expand Down Expand Up @@ -880,6 +886,15 @@ class TOPPFileConverter :
SqMassFile sqm;
sqm.store(out, exp);
}
else if (out_type == FileTypes::OMS)
{
if (in_type != FileTypes::FEATUREXML)
{
OPENMS_LOG_ERROR << "Incompatible input data: FileConverter can only convert featureXML files to oms format.";
return INCOMPATIBLE_INPUT_DATA;
}
OMSFile().store(out, fm);
oliveralka marked this conversation as resolved.
Show resolved Hide resolved
}
else
{
writeLog_("Unknown output file type given. Aborting!");
Expand Down