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Commit 0179a734 authored by Sascha Steinbiss's avatar Sascha Steinbiss
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allow to exclude attributes from GFF3 output

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uk/ac/sanger/artemis/io/GFFStreamFeature.java
+ 27
− 0
View file @ 0179a734
...@@ -27,8 +27,10 @@ package uk.ac.sanger.artemis.io; ...@@ -27,8 +27,10 @@ package uk.ac.sanger.artemis.io;
import java.util.Hashtable; import java.util.Hashtable;
import java.util.HashSet;
import java.util.Enumeration; import java.util.Enumeration;
import java.util.List; import java.util.List;
import java.util.Set;
import java.util.StringTokenizer; import java.util.StringTokenizer;
import java.util.Vector; import java.util.Vector;
import java.io.IOException; import java.io.IOException;
...@@ -113,6 +115,28 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -113,6 +115,28 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{ "\n", "%5C" } // new-line { "\n", "%5C" } // new-line
}; };
private static Set<String> attrs_to_filter = new HashSet<String>();
/**
* Registers an attribute not to be included in the GFF3 output for
* GFFStreamFeatures
* @param attr The GFF3 attribute to remove
**/
public static void removeAttribute(String attr)
{
attrs_to_filter.add(attr);
}
/**
* Registers an attribute to be included in the GFF3 output for
* GFFStreamFeatures
* @param attr The GFF3 attribute to include
**/
public static void includeAttribute(String attr)
{
attrs_to_filter.remove(attr);
}
/** /**
* Create a new GFFStreamFeature object. The feature should be added * Create a new GFFStreamFeature object. The feature should be added
* to an Entry (with Entry.add()). * to an Entry (with Entry.add()).
...@@ -893,6 +917,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -893,6 +917,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(lname) if(lname)
continue; continue;
if(attrs_to_filter.contains(this_qualifier.getName()))
continue;
if( (this_qualifier.getName().equals("private") && System.getProperty("noprivate") != null) || if( (this_qualifier.getName().equals("private") && System.getProperty("noprivate") != null) ||
(this_qualifier.getName().equals("history") && System.getProperty("nohistory") != null) ) (this_qualifier.getName().equals("history") && System.getProperty("nohistory") != null) )
continue; continue;
......
uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
+ 66
− 53
View file @ 0179a734
...@@ -42,11 +42,11 @@ import uk.ac.sanger.artemis.Options; ...@@ -42,11 +42,11 @@ import uk.ac.sanger.artemis.Options;
public class ReadAndWriteEntry public class ReadAndWriteEntry
{ {
private static org.apache.log4j.Logger logger4j = private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(ReadAndWriteEntry.class); org.apache.log4j.Logger.getLogger(ReadAndWriteEntry.class);
private static DatabaseEntrySource ENTRY_SOURCE; private static DatabaseEntrySource ENTRY_SOURCE;
/** /**
* Read from the database, given a srcFeature uniquename * Read from the database, given a srcFeature uniquename
* @param uniqueName * @param uniqueName
...@@ -56,7 +56,7 @@ public class ReadAndWriteEntry ...@@ -56,7 +56,7 @@ public class ReadAndWriteEntry
* @throws IOException * @throws IOException
*/ */
public static Entry readEntryFromDatabase(final String uniqueName, public static Entry readEntryFromDatabase(final String uniqueName,
DatabaseEntrySource entry_source) DatabaseEntrySource entry_source)
throws OutOfRangeException, NoSequenceException, IOException throws OutOfRangeException, NoSequenceException, IOException
{ {
if(entry_source == null) if(entry_source == null)
...@@ -71,23 +71,23 @@ public class ReadAndWriteEntry ...@@ -71,23 +71,23 @@ public class ReadAndWriteEntry
if(!entry_source.setLocation(promptUser)) if(!entry_source.setLocation(promptUser))
return null; return null;
} }
String url = (String)entry_source.getLocation(); String url = (String)entry_source.getLocation();
int index = url.indexOf("?"); int index = url.indexOf("?");
String userName = url.substring(index+1).trim(); String userName = url.substring(index+1).trim();
if(userName.startsWith("user=")) if(userName.startsWith("user="))
userName = userName.substring(5); userName = userName.substring(5);
final String srcFeatureId = getFeatureId(entry_source, uniqueName); final String srcFeatureId = getFeatureId(entry_source, uniqueName);
final InputStreamProgressListener stream_progress_listener = final InputStreamProgressListener stream_progress_listener =
new InputStreamProgressListener() new InputStreamProgressListener()
{ {
public void progressMade(final InputStreamProgressEvent event) public void progressMade(final InputStreamProgressEvent event)
{ {
final int char_count = event.getCharCount(); final int char_count = event.getCharCount();
if(char_count != -1) if(char_count != -1)
logger4j.debug("chars read so far: " + char_count); logger4j.debug("chars read so far: " + char_count);
} }
public void progressMade(String progress) public void progressMade(String progress)
...@@ -95,10 +95,10 @@ public class ReadAndWriteEntry ...@@ -95,10 +95,10 @@ public class ReadAndWriteEntry
logger4j.debug(progress); logger4j.debug(progress);
} }
}; };
return entry_source.getEntry(srcFeatureId, userName, return entry_source.getEntry(srcFeatureId, userName,
stream_progress_listener); stream_progress_listener);
} }
/** /**
* Read from the database, given a srcFeature uniquename * Read from the database, given a srcFeature uniquename
* @param uniqueName * @param uniqueName
...@@ -107,12 +107,12 @@ public class ReadAndWriteEntry ...@@ -107,12 +107,12 @@ public class ReadAndWriteEntry
* @throws NoSequenceException * @throws NoSequenceException
* @throws IOException * @throws IOException
*/ */
public static Entry readEntryFromDatabase(final String uniqueName) public static Entry readEntryFromDatabase(final String uniqueName)
throws OutOfRangeException, NoSequenceException, IOException throws OutOfRangeException, NoSequenceException, IOException
{ {
return readEntryFromDatabase(uniqueName, null); return readEntryFromDatabase(uniqueName, null);
} }
/** /**
* Write entry to a file * Write entry to a file
* @param entry * @param entry
...@@ -120,7 +120,7 @@ public class ReadAndWriteEntry ...@@ -120,7 +120,7 @@ public class ReadAndWriteEntry
* @param flatten Flatten the gene model and combine the qualifiers if true. * @param flatten Flatten the gene model and combine the qualifiers if true.
* If false it will write all features and qualifiers out. * If false it will write all features and qualifiers out.
* @param ignore obsolete features if true * @param ignore obsolete features if true
* @param force invalid qualifiers and any features with invalid keys will * @param force invalid qualifiers and any features with invalid keys will
* be quietly thrown away when saving. * be quietly thrown away when saving.
* @param include_diana_extensions false if writing EMBL submission format. * @param include_diana_extensions false if writing EMBL submission format.
* @param destination_type Should be one of EMBL_FORMAT, GENBANK_FORMAT, * @param destination_type Should be one of EMBL_FORMAT, GENBANK_FORMAT,
...@@ -137,7 +137,7 @@ public class ReadAndWriteEntry ...@@ -137,7 +137,7 @@ public class ReadAndWriteEntry
final boolean force, final boolean force,
final boolean include_diana_extensions, final boolean include_diana_extensions,
final int destination_type, final int destination_type,
final JFrame parent) final JFrame parent)
throws IOException, EntryInformationException throws IOException, EntryInformationException
{ {
GeneUtils.lazyLoadAll(entry, parent); GeneUtils.lazyLoadAll(entry, parent);
...@@ -148,15 +148,15 @@ public class ReadAndWriteEntry ...@@ -148,15 +148,15 @@ public class ReadAndWriteEntry
final FeatureVector features = entry.getAllFeatures(); final FeatureVector features = entry.getAllFeatures();
for(int i=0; i<features.size(); i++) for(int i=0; i<features.size(); i++)
addAllKeysQualifiers(artemis_entry_information, features.elementAt(i).getEmblFeature()); addAllKeysQualifiers(artemis_entry_information, features.elementAt(i).getEmblFeature());
if(entry.getEMBLEntry() instanceof GFFDocumentEntry) if(entry.getEMBLEntry() instanceof GFFDocumentEntry)
addQualifierToEntryInfo(artemis_entry_information, addQualifierToEntryInfo(artemis_entry_information,
(String)PublicDBDocumentEntry.getDatabaseQualifiersToRemove()[0]); (String)PublicDBDocumentEntry.getDatabaseQualifiersToRemove()[0]);
} }
PublicDBDocumentEntry.IGNORE_OBSOLETE_FEATURES = ignoreObsolete; PublicDBDocumentEntry.IGNORE_OBSOLETE_FEATURES = ignoreObsolete;
if(destination_type == DocumentEntryFactory.EMBL_FORMAT && if(destination_type == DocumentEntryFactory.EMBL_FORMAT &&
(entry.getHeaderText() == null || (entry.getHeaderText() == null ||
entry.getHeaderText().equals("") || entry.getHeaderText().equals("") ||
entry.getHeaderText().startsWith("#"))) entry.getHeaderText().startsWith("#")))
{ {
...@@ -169,9 +169,9 @@ public class ReadAndWriteEntry ...@@ -169,9 +169,9 @@ public class ReadAndWriteEntry
ind = name.lastIndexOf(".embl"); ind = name.lastIndexOf(".embl");
if(ind > -1) if(ind > -1)
name = name.substring(0, ind); name = name.substring(0, ind);
} }
int length = entry.getBases().getLength(); int length = entry.getBases().getLength();
String header = "ID "+name+"; SV ; ; ; ; ; "+length+" BP."; String header = "ID "+name+"; SV ; ; ; ; ; "+length+" BP.";
if(entry.getFeatureCount() > 0) if(entry.getFeatureCount() > 0)
...@@ -185,10 +185,10 @@ public class ReadAndWriteEntry ...@@ -185,10 +185,10 @@ public class ReadAndWriteEntry
else else
entry.saveStandardOnly(file, destination_type, force); entry.saveStandardOnly(file, destination_type, force);
} }
/** /**
* Add all keys and qualifiers for a given feature to the EntryInformation * Add all keys and qualifiers for a given feature to the EntryInformation
* @param entry_information * @param entry_information
* @param feature * @param feature
*/ */
...@@ -196,18 +196,18 @@ public class ReadAndWriteEntry ...@@ -196,18 +196,18 @@ public class ReadAndWriteEntry
final Feature feature) final Feature feature)
{ {
Key new_key = feature.getKey(); Key new_key = feature.getKey();
new_key = PublicDBDocumentEntry.mapKeys(new_key); new_key = PublicDBDocumentEntry.mapKeys(new_key);
boolean keyAdded = false; boolean keyAdded = false;
if(!entry_information.isValidKey(new_key)) if(!entry_information.isValidKey(new_key))
{ {
entry_information.addKey(new_key); entry_information.addKey(new_key);
keyAdded = true; keyAdded = true;
} }
final QualifierVector feature_qualifiers = feature.getQualifiers(); final QualifierVector feature_qualifiers = feature.getQualifiers();
// check the qualifiers // check the qualifiers
for(int i = 0 ; i < feature_qualifiers.size() ; ++i) for(int i = 0 ; i < feature_qualifiers.size() ; ++i)
{ {
...@@ -216,10 +216,10 @@ public class ReadAndWriteEntry ...@@ -216,10 +216,10 @@ public class ReadAndWriteEntry
if(!entry_information.isValidQualifier(this_qualifier_name) || if(!entry_information.isValidQualifier(this_qualifier_name) ||
!entry_information.isValidQualifier(new_key, this_qualifier_name) || !entry_information.isValidQualifier(new_key, this_qualifier_name) ||
keyAdded) keyAdded)
{ {
QualifierInfo qualifierInfo = entry_information.getQualifierInfo(this_qualifier_name); QualifierInfo qualifierInfo = entry_information.getQualifierInfo(this_qualifier_name);
if(qualifierInfo == null) if(qualifierInfo == null)
{ {
KeyVector keys = new KeyVector(); KeyVector keys = new KeyVector();
...@@ -234,14 +234,14 @@ public class ReadAndWriteEntry ...@@ -234,14 +234,14 @@ public class ReadAndWriteEntry
e.printStackTrace(); e.printStackTrace();
} }
} }
if(qualifierInfo.getValidKeys() != null) if(qualifierInfo.getValidKeys() != null)
qualifierInfo.getValidKeys().add(new_key); qualifierInfo.getValidKeys().add(new_key);
} }
} }
} }
protected static void addQualifierToEntryInfo(final EntryInformation entry_information, protected static void addQualifierToEntryInfo(final EntryInformation entry_information,
final String qualifier_name) final String qualifier_name)
{ {
...@@ -257,7 +257,7 @@ public class ReadAndWriteEntry ...@@ -257,7 +257,7 @@ public class ReadAndWriteEntry
e.printStackTrace(); e.printStackTrace();
} }
} }
/** /**
* Get feature id * Get feature id
* @param entry_source * @param entry_source
...@@ -271,7 +271,7 @@ public class ReadAndWriteEntry ...@@ -271,7 +271,7 @@ public class ReadAndWriteEntry
org.gmod.schema.sequence.Feature feature = doc.getFeatureByUniquename(srcUniqueName); org.gmod.schema.sequence.Feature feature = doc.getFeatureByUniquename(srcUniqueName);
return Integer.toString(feature.getFeatureId()); return Integer.toString(feature.getFeatureId());
} }
/** /**
* return the ENTRY_SOURCE * return the ENTRY_SOURCE
*/ */
...@@ -287,17 +287,18 @@ public class ReadAndWriteEntry ...@@ -287,17 +287,18 @@ public class ReadAndWriteEntry
String names[]; String names[];
boolean flatten = true; boolean flatten = true;
boolean ignoreObsolete = true; boolean ignoreObsolete = true;
if( (args != null && args.length == 1 && args[0].startsWith("-h")) || if( (args != null && args.length == 1 && args[0].startsWith("-h")) ||
(args == null || args.length < 1)) (args == null || args.length < 1))
{ {
System.out.println("-h\tshow help"); System.out.println("-h\tshow help");
System.out.println("-f\t[y|n] flatten the gene model, default is y"); System.out.println("-f\t[y|n] flatten the gene model, default is y");
System.out.println("-flt\tspace separated list of qualifiers to ignore (GFF only)");
System.out.println("-i\t[y|n] ignore obsolete features, default is y"); System.out.println("-i\t[y|n] ignore obsolete features, default is y");
System.out.println("-s\tspace separated list of sequences to read and write out"); System.out.println("-s\tspace separated list of sequences to read and write out");
System.out.println("-o\t[EMBL|GFF] output format, default is EMBL"); System.out.println("-o\t[EMBL|GFF] output format, default is EMBL");
// note that read_only and noprompt -D parameters redundant now // note that read_only and noprompt -D parameters redundant now
System.out.println("Advanced parameters:"); System.out.println("Advanced parameters:");
System.out.println("-l\tlocation of EMBL mapping files (qualifier_mapping and key_mapping)"); System.out.println("-l\tlocation of EMBL mapping files (qualifier_mapping and key_mapping)");
...@@ -310,11 +311,11 @@ public class ReadAndWriteEntry ...@@ -310,11 +311,11 @@ public class ReadAndWriteEntry
System.out.println("-p\tthe password for connecting to the Chado database"); System.out.println("-p\tthe password for connecting to the Chado database");
System.out.println("-fp\t the file path (the folder you want to save the files in)"); System.out.println("-fp\t the file path (the folder you want to save the files in)");
System.out.println("-np\t[y|n] do not write out private qualifiers, default is y"); System.out.println("-np\t[y|n] do not write out private qualifiers, default is y");
System.exit(0); System.exit(0);
} }
names = args; names = args;
int format = DocumentEntryFactory.EMBL_FORMAT; int format = DocumentEntryFactory.EMBL_FORMAT;
boolean include_diana_extensions = true; boolean include_diana_extensions = true;
...@@ -322,9 +323,9 @@ public class ReadAndWriteEntry ...@@ -322,9 +323,9 @@ public class ReadAndWriteEntry
boolean gzip = true; boolean gzip = true;
boolean noprivates = true; boolean noprivates = true;
boolean removeProductForPseudo = false; boolean removeProductForPseudo = false;
String filePath = ""; String filePath = "";
for(int i = 0; i < args.length; i++) for(int i = 0; i < args.length; i++)
{ {
String key = args[i].toLowerCase(); String key = args[i].toLowerCase();
...@@ -366,7 +367,7 @@ public class ReadAndWriteEntry ...@@ -366,7 +367,7 @@ public class ReadAndWriteEntry
if(i + 1 < args.length && args[i + 1].toLowerCase().equals("y")) if(i + 1 < args.length && args[i + 1].toLowerCase().equals("y"))
LocalAndRemoteFileManager.domainLoad.setSelected(true); LocalAndRemoteFileManager.domainLoad.setSelected(true);
} }
// GSV :: added these command-line parameters // GSV :: added these command-line parameters
// note that read_only and noprompt -D parameters redundant now // note that read_only and noprompt -D parameters redundant now
else if (key.equals("-u")) else if (key.equals("-u"))
...@@ -391,10 +392,10 @@ public class ReadAndWriteEntry ...@@ -391,10 +392,10 @@ public class ReadAndWriteEntry
filePath = args[i + 1]; filePath = args[i + 1];
} }
} }
// run this after all the system properties have been set // run this after all the system properties have been set
UI.initalise(); UI.initalise();
java.util.Vector<String> files = null; java.util.Vector<String> files = null;
for(int i = 0; i < args.length; i++) for(int i = 0; i < args.length; i++)
{ {
...@@ -407,6 +408,18 @@ public class ReadAndWriteEntry ...@@ -407,6 +408,18 @@ public class ReadAndWriteEntry
if(args[j].startsWith("-")) if(args[j].startsWith("-"))
break; break;
files.add(args[j]); files.add(args[j]);
i++;
}
}
else if(args[i].toLowerCase().equals("-flt"))
{
for(int j = i + 1; j < args.length; j++)
{
if(args[j].startsWith("-")) {
break;
}
GFFStreamFeature.removeAttribute(args[j]);
i++;
} }
} }
else if(args[i].startsWith("-")) else if(args[i].startsWith("-"))
...@@ -426,7 +439,7 @@ public class ReadAndWriteEntry ...@@ -426,7 +439,7 @@ public class ReadAndWriteEntry
names = new String[files.size()]; names = new String[files.size()];
files.toArray(names); files.toArray(names);
} }
if(filePath.length() != 0) if(filePath.length() != 0)
{ {
filePath += "/"; filePath += "/";
...@@ -437,19 +450,19 @@ public class ReadAndWriteEntry ...@@ -437,19 +450,19 @@ public class ReadAndWriteEntry
if(noprivates) if(noprivates)
System.setProperty("noprivate", "true"); System.setProperty("noprivate", "true");
for(int i=0;i < names.length; i++) for(int i=0;i < names.length; i++)
{ {
System.out.println("read :: "+names[i]+" write :: "+names[i]+suffix); System.out.println("read :: "+names[i]+" write :: "+names[i]+suffix);
logger4j.info("read :: "+names[i]+" write :: "+names[i]+suffix); logger4j.info("read :: "+names[i]+" write :: "+names[i]+suffix);
Entry entry = ReadAndWriteEntry.readEntryFromDatabase(names[i], ENTRY_SOURCE); Entry entry = ReadAndWriteEntry.readEntryFromDatabase(names[i], ENTRY_SOURCE);
DocumentEntryFactory.REMOVE_PRODUCT_FROM_PSEUDOGENE = removeProductForPseudo; DocumentEntryFactory.REMOVE_PRODUCT_FROM_PSEUDOGENE = removeProductForPseudo;
try try
{ {
ReadAndWriteEntry.writeDatabaseEntryToFile( ReadAndWriteEntry.writeDatabaseEntryToFile(
entry, new File(filePath + names[i]+suffix), flatten, ignoreObsolete, entry, new File(filePath + names[i]+suffix), flatten, ignoreObsolete,
false, include_diana_extensions, format, null); false, include_diana_extensions, format, null);
System.out.println("done"); System.out.println("done");
logger4j.info("done"); logger4j.info("done");
...@@ -458,10 +471,10 @@ public class ReadAndWriteEntry ...@@ -458,10 +471,10 @@ public class ReadAndWriteEntry
{ {
String label = "Destination format can't handle all keys/qualifiers - continue?"; String label = "Destination format can't handle all keys/qualifiers - continue?";
boolean canContinue = UI.booleanUserInput(label, eie.getMessage()); boolean canContinue = UI.booleanUserInput(label, eie.getMessage());
if (canContinue) if (canContinue)
{ {
ReadAndWriteEntry.writeDatabaseEntryToFile(entry, new File(filePath + names[i] + suffix), ReadAndWriteEntry.writeDatabaseEntryToFile(entry, new File(filePath + names[i] + suffix),
flatten, ignoreObsolete, true, flatten, ignoreObsolete, true,
include_diana_extensions, format, null); include_diana_extensions, format, null);
System.out.println("done"); System.out.println("done");
...@@ -477,5 +490,5 @@ public class ReadAndWriteEntry ...@@ -477,5 +490,5 @@ public class ReadAndWriteEntry
} }
System.exit(0); System.exit(0);
} }
} }
\ No newline at end of file
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