Changeset 5771
- Timestamp:
- Sep 29, 2011, 1:48:47 PM (11 years ago)
- Location:
- trunk
- Files:
-
- 4 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/data/plugin_configfile.xml
r5770 r5771 934 934 <configuration pluginClassName="net.sf.basedb.plugins.gtf.GtfReporterImporter"> 935 935 <configname>gene_id (no prefix)</configname> 936 <description>A configuration that uses the gene_id instead of the transcript_id as reporter id.</description> 936 <description>A configuration that uses the <gene_id> as reporter id.</description> 937 <parameter> 938 <name>reporterIdColumnMapping</name> 939 <label>External ID</label> 940 <description>Mapping that picks the reporter's external ID from the data columns. For example: \ID\</description> 941 <class>java.lang.String</class> 942 <value>\<gene_id>\</value> 943 </parameter> 937 944 <parameter> 938 945 <name>trimQuotes</name> … … 950 957 </parameter> 951 958 <parameter> 952 <name>reporterIdColumnMapping</name>953 <label>External ID</label>954 <description>Mapping that picks the reporter's external ID from the data columns. For example: \ID\</description>955 <class>java.lang.String</class>956 <value>\<gene_id>\</value>957 </parameter>958 <parameter>959 959 <name>minDataColumns</name> 960 960 <label>Min data columns</label> … … 986 986 </parameter> 987 987 <parameter> 988 <name>extendedColumnMapping.chromosome</name> 989 <label>Chromosome</label> 990 <description>The chromosome from which the reporter is derived</description> 991 <class>java.lang.String</class> 992 <value>\<seqname>\</value> 993 </parameter> 994 <parameter> 995 <name>decimalSeparator</name> 996 <label>Decimal separator</label> 997 <description>The decimal separator used in numeric values, if not specified dot is assumed.</description> 998 <class>java.lang.String</class> 999 <value>dot</value> 1000 </parameter> 1001 <parameter> 988 1002 <name>dataSplitterRegexp</name> 989 1003 <label>Data splitter</label> … … 993 1007 </parameter> 994 1008 <parameter> 995 <name> decimalSeparator</name>996 <label> Decimal separator</label>997 <description> The decimal separator used in numeric values, if not specified dot is assumed.</description>998 <class>java.lang.String</class> 999 <value> dot</value>1009 <name>symbolColumnMapping</name> 1010 <label>Gene symbol</label> 1011 <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description> 1012 <class>java.lang.String</class> 1013 <value>\<gene_id>\</value> 1000 1014 </parameter> 1001 1015 </configuration> 1002 1016 <configuration pluginClassName="net.sf.basedb.plugins.gtf.GtfReporterImporter"> 1003 <configname>transcript_id@ chr(no prefix)</configname>1017 <configname>transcript_id@seqname (no prefix)</configname> 1004 1018 <description>A configuration that uses the <transcript_id>@<seqname> as reporter id. <seqname> is usually the chromosome ID (eg. chr1).</description> 1005 1019 <parameter> 1006 <name> dataHeaderRegexp</name>1007 <label> Data header</label>1008 <description> A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>1009 <class>java.lang.String</class> 1010 <value> <seqname>\t.*<transcript_id>.*</value>1020 <name>reporterIdColumnMapping</name> 1021 <label>External ID</label> 1022 <description>Mapping that picks the reporter's external ID from the data columns. For example: \ID\</description> 1023 <class>java.lang.String</class> 1024 <value>\<transcript_id>\@\<seqname>\</value> 1011 1025 </parameter> 1012 1026 <parameter> … … 1018 1032 </parameter> 1019 1033 <parameter> 1020 <name> reporterIdColumnMapping</name>1021 <label> External ID</label>1022 <description> Mapping that picks the reporter's external ID from the data columns. For example: \ID\</description>1023 <class>java.lang.String</class> 1024 <value> \<transcript_id>\@\<seqname>\</value>1034 <name>dataHeaderRegexp</name> 1035 <label>Data header</label> 1036 <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description> 1037 <class>java.lang.String</class> 1038 <value><seqname>\t.*<transcript_id>.*</value> 1025 1039 </parameter> 1026 1040 <parameter> … … 1054 1068 </parameter> 1055 1069 <parameter> 1070 <name>extendedColumnMapping.chromosome</name> 1071 <label>Chromosome</label> 1072 <description>The chromosome from which the reporter is derived</description> 1073 <class>java.lang.String</class> 1074 <value>\<seqname>\</value> 1075 </parameter> 1076 <parameter> 1077 <name>decimalSeparator</name> 1078 <label>Decimal separator</label> 1079 <description>The decimal separator used in numeric values, if not specified dot is assumed.</description> 1080 <class>java.lang.String</class> 1081 <value>dot</value> 1082 </parameter> 1083 <parameter> 1056 1084 <name>dataSplitterRegexp</name> 1057 1085 <label>Data splitter</label> … … 1061 1089 </parameter> 1062 1090 <parameter> 1063 <name>extendedColumnMapping.chromosome</name>1064 <label>Chromosome</label>1065 <description>The chromosome from which the reporter is derived</description>1066 <class>java.lang.String</class>1067 <value>\<seqname>\</value>1068 </parameter>1069 <parameter>1070 <name>decimalSeparator</name>1071 <label>Decimal separator</label>1072 <description>The decimal separator used in numeric values, if not specified dot is assumed.</description>1073 <class>java.lang.String</class>1074 <value>dot</value>1075 </parameter>1076 <parameter>1077 1091 <name>symbolColumnMapping</name> 1078 1092 <label>Gene symbol</label> … … 1083 1097 </configuration> 1084 1098 <configuration pluginClassName="net.sf.basedb.plugins.gtf.GtfReporterMapImporter"> 1085 <configname>transcript_id (no prefix)</configname>1086 <description>A configuration that uses the transcript_id (no prefix) as reporter and feature id.</description>1099 <configname>transcript_id@seqname (no prefix)</configname> 1100 <description>A configuration that uses <transcript_id>@<seqname> as reporter and feature id. <seqname> is usually the chromosome ID (eg. chr1).</description> 1087 1101 <parameter> 1088 1102 <name>reporterIdColumnMapping</name> … … 1107 1121 </parameter> 1108 1122 <parameter> 1123 <name>minDataColumns</name> 1124 <label>Min data columns</label> 1125 <description>The minimum number of columns for a line to be counted as a data line.</description> 1126 <class>java.lang.Integer</class> 1127 <value>4</value> 1128 </parameter> 1129 <parameter> 1109 1130 <name>featureIdentification</name> 1110 1131 <label /> … … 1119 1140 allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description> 1120 1141 <class>java.lang.String</class> 1121 <value> disallow</value>1142 <value>allow</value> 1122 1143 </parameter> 1123 1144 <parameter> … … 1131 1152 <name>featureIdColumnMapping</name> 1132 1153 <label>Feature ID</label> 1133 <description>Mapping that picks the feature's ID from the data columns. This column is only used when the array design uses the FEATURE_ID method for identifying features. In the other cases, the value is just stored as it is.For example: \Feature ID\</description>1134 <class>java.lang.String</class> 1135 <value>\<transcript_id>\ </value>1154 <description>Mapping that picks the feature's ID from the data columns. For example: \<transcript_id>\</description> 1155 <class>java.lang.String</class> 1156 <value>\<transcript_id>\@\<seqname>\</value> 1136 1157 </parameter> 1137 1158 <parameter> … … 1145 1166 <configuration pluginClassName="net.sf.basedb.plugins.gtf.GtfReporterMapImporter"> 1146 1167 <configname>gene_id (no prefix)</configname> 1147 <description>A configuration that uses the gene_id (no prefix) as reporter id and transcript_id as feature id. Note that gene_idmay not be unique so it is not recommended to use that as feature id.</description>1168 <description>A configuration that uses the <gene_id> as reporter id and <transcript_id>@<seqname> as feature id. Note that <gene_id> may not be unique so it is not recommended to use that as feature id.</description> 1148 1169 <parameter> 1149 1170 <name>reporterIdColumnMapping</name> … … 1152 1173 <class>java.lang.String</class> 1153 1174 <value>\<gene_id>\</value> 1175 </parameter> 1176 <parameter> 1177 <name>dataHeaderRegexp</name> 1178 <label>Data header</label> 1179 <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description> 1180 <class>java.lang.String</class> 1181 <value><seqname>\t.*<gene_id>.*</value> 1154 1182 </parameter> 1155 1183 <parameter> … … 1161 1189 </parameter> 1162 1190 <parameter> 1163 <name> dataHeaderRegexp</name>1164 <label> Data header</label>1165 <description> A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>1166 <class>java.lang. String</class>1167 <value> <seqname>\t.*<gene_id>.*</value>1191 <name>minDataColumns</name> 1192 <label>Min data columns</label> 1193 <description>The minimum number of columns for a line to be counted as a data line.</description> 1194 <class>java.lang.Integer</class> 1195 <value>4</value> 1168 1196 </parameter> 1169 1197 <parameter> … … 1180 1208 allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description> 1181 1209 <class>java.lang.String</class> 1182 <value> disallow</value>1210 <value>allow</value> 1183 1211 </parameter> 1184 1212 <parameter> … … 1192 1220 <name>featureIdColumnMapping</name> 1193 1221 <label>Feature ID</label> 1194 <description>Mapping that picks the feature's ID from the data columns. This column is only used when the array design uses the FEATURE_ID method for identifying features. In the other cases, the value is just stored as it is.For example: \Feature ID\</description>1195 <class>java.lang.String</class> 1196 <value>\<transcript_id>\ </value>1222 <description>Mapping that picks the feature's ID from the data columns. For example: \<transcript_id>\</description> 1223 <class>java.lang.String</class> 1224 <value>\<transcript_id>\@\<seqname>\</value> 1197 1225 </parameter> 1198 1226 <parameter> -
trunk/src/plugins/core/net/sf/basedb/plugins/ReporterFlatFileImporter.java
r5759 r5771 851 851 // Column mappings 852 852 parameters.add(mappingSection); 853 parameters.add(c omplexMappings);853 parameters.add(cloneParameterWithDefaultValue(complexMappings)); 854 854 parameters.addAll(getAllColumnMappings(reporterListContext)); 855 855 … … 917 917 // Column mappings 918 918 parameters.add(mappingSection); 919 parameters.add(c omplexMappings);919 parameters.add(cloneParameterWithDefaultValue(complexMappings)); 920 920 parameters.addAll(getAllColumnMappings(false)); 921 921 -
trunk/src/plugins/core/net/sf/basedb/plugins/gtf/GtfReporterMapImporter.java
r5764 r5771 50 50 /** 51 51 Import features to an array design from a GTF file. The default 52 settings use transcript_id as the feature id and reporter id. This52 settings use transcript_id+seqname as the feature id and reporter id. This 53 53 can be changed by user configuration, but it is recommended that 54 transcript_id is used as feature id since other values may not be55 unique.54 transcript_id+seqname is used as feature id since other combinations of 55 values may not be unique in raw data files. 56 56 57 57 @author Nicklas … … 79 79 "Feature ID", 80 80 "Mapping that picks the feature's ID from the data columns. " + 81 "For example: \\<transcript_id>\\ ",81 "For example: \\<transcript_id>\\@\\<seqname>\\", 82 82 new StringParameterType(255, null, true) 83 83 ); … … 254 254 // Column mappings 255 255 parameters.add(mappingSection); 256 parameters.add(c omplexMappings);256 parameters.add(cloneParameterWithDefaultValue(complexMappings)); 257 257 parameters.addAll(getAllColumnMappings()); 258 258 -
trunk/src/test/TestGtfImporters.java
r5770 r5771 65 65 TestReporter.test_list(35); 66 66 67 /* 67 68 68 // Test reporter map importer 69 69 int arrayDesignId = TestArrayDesign.test_create(PlatformVariant.SEQUENCING_EXPRESSION, false); … … 75 75 TestArrayDesign.write_feature_header(); 76 76 TestArrayDesign.test_list_features(arrayDesignId, 35); 77 */ 77 78 78 if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter(); 79 //TestArrayDesign.test_delete(arrayDesignId);79 TestArrayDesign.test_delete(arrayDesignId); 80 80 // Delete reporters 81 81 int deleteReporterJobId = test_create_reporter_job(gtfReporterImporterId, fileId, "delete"); … … 84 84 TestJob.test_delete(reporterJobId); 85 85 TestJob.test_delete(deleteReporterJobId); 86 //TestJob.test_delete(featureJobId);87 //TestPluginConfiguration.test_delete(featureConfigurationId);86 TestJob.test_delete(featureJobId); 87 TestPluginConfiguration.test_delete(featureConfigurationId); 88 88 TestFile.test_delete(fileId); 89 89 … … 160 160 { 161 161 ParameterType pt = pp.getParameterType(); 162 System.out.println("\tParameter:\t"+pp.getName() + "\t" + pp.getLabel() + "\t" + pt );162 System.out.println("\tParameter:\t"+pp.getName() + "\t" + pp.getLabel() + "\t" + pt + "\t" + pp.getDefaultValue() ); 163 163 } 164 164 }
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