Accept to deal with sequence in lower case
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@217 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
122
.cproject
Normal file
122
.cproject
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@ -0,0 +1,122 @@
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<configuration artifactName="ecoPCR" buildProperties="" id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067" name="MacOSX GCC" parent="org.eclipse.cdt.build.core.emptycfg">
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<tool id="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base.815782479" name="MacOS X C++ Linker" superClass="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base"/>
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<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base.1142106025" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base"/>
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<tool id="cdt.managedbuild.tool.gnu.c.compiler.macosx.base.845498516" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.macosx.base"/>
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<parser enabled="true"/>
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
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<parser enabled="true"/>
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
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</cconfiguration>
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</storageModule>
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<storageModule moduleId="cdtBuildSystem" version="4.0.0">
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<project id="ecoPCR.null.1320766773" name="ecoPCR"/>
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</storageModule>
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</cproject>
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83
.project
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83
.project
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@ -0,0 +1,83 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<projectDescription>
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<name>ecoPCR</name>
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<comment></comment>
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<projects>
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</projects>
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<buildSpec>
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<buildCommand>
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<name>org.python.pydev.PyDevBuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
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<triggers>clean,full,incremental,</triggers>
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<arguments>
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<dictionary>
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<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
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<value>all</value>
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</dictionary>
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<dictionary>
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<key>?name?</key>
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<value></value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
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<value>false</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.enableFullBuild</key>
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<value>true</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
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<value>true</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
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<value>clean</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.append_environment</key>
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<value>true</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.contents</key>
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<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
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<value>true</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.buildArguments</key>
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<value></value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.buildCommand</key>
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<value>make</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
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<value>all</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.stopOnError</key>
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<value>true</value>
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</dictionary>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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</buildSpec>
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<natures>
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<nature>org.eclipse.cdt.core.cnature</nature>
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<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
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<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
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<nature>org.python.pydev.pythonNature</nature>
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</natures>
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</projectDescription>
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7
.pydevproject
Normal file
7
.pydevproject
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@ -0,0 +1,7 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<?eclipse-pydev version="1.0"?>
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<pydev_project>
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<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.4</pydev_property>
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<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
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</pydev_project>
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BIN
src/ecoPCR.gz
Executable file
BIN
src/ecoPCR.gz
Executable file
Binary file not shown.
BIN
src/ecofind.gz
Executable file
BIN
src/ecofind.gz
Executable file
Binary file not shown.
BIN
src/ecogrep
Executable file
BIN
src/ecogrep
Executable file
Binary file not shown.
BIN
src/ecogrep.gz
Executable file
BIN
src/ecogrep.gz
Executable file
Binary file not shown.
BIN
src/ecoisundertaxon
Executable file
BIN
src/ecoisundertaxon
Executable file
Binary file not shown.
@ -4,6 +4,7 @@
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#include <zlib.h>
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#include <string.h>
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#include <stdio.h>
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#include <ctype.h>
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static FILE *open_seqfile(const char *prefix,int32_t index);
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@ -11,32 +12,32 @@ static FILE *open_seqfile(const char *prefix,int32_t index);
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ecoseq_t *new_ecoseq()
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{
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void *tmp;
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tmp = ECOMALLOC(sizeof(ecoseq_t),"Allocate new ecoseq structure");
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return tmp;
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}
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int32_t delete_ecoseq(ecoseq_t * seq)
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{
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if (seq)
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{
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if (seq->AC)
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ECOFREE(seq->AC,"Free sequence AC");
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if (seq->DE)
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ECOFREE(seq->DE,"Free sequence DE");
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if (seq->SQ)
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ECOFREE(seq->SQ,"Free sequence SQ");
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ECOFREE(seq,"Free sequence structure");
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return 0;
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}
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return 1;
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}
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@ -49,9 +50,9 @@ ecoseq_t *new_ecoseq_with_data( char *AC,
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ecoseq_t *tmp;
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int32_t lstr;
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tmp = new_ecoseq();
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tmp->taxid=taxid_idx;
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if (AC)
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{
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lstr =strlen(AC);
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@ -97,12 +98,14 @@ ecoseq_t *readnext_ecoseq(FILE *f)
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int32_t comp_status;
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unsigned long int seqlength;
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int32_t rs;
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char *c;
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int32_t i;
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raw = read_ecorecord(f,&rs);
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if (!raw)
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return NULL;
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if (is_big_endian())
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{
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raw->CSQ_length = swap_int32_t(raw->CSQ_length);
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@ -110,44 +113,48 @@ ecoseq_t *readnext_ecoseq(FILE *f)
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raw->SQ_length = swap_int32_t(raw->SQ_length);
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raw->taxid = swap_int32_t(raw->taxid);
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}
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seq = new_ecoseq();
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seq->taxid = raw->taxid;
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seq->AC = ECOMALLOC(strlen(raw->AC) +1,
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"Allocate Sequence Accesion number");
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strncpy(seq->AC,raw->AC,strlen(raw->AC));
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seq->DE = ECOMALLOC(raw->DE_length+1,
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"Allocate Sequence definition");
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strncpy(seq->DE,raw->data,raw->DE_length);
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seqlength = seq->SQ_length = raw->SQ_length;
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compressed = raw->data + raw->DE_length;
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seq->SQ = ECOMALLOC(seqlength+1,
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"Allocate sequence buffer");
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comp_status = uncompress((unsigned char*)seq->SQ,
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&seqlength,
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(unsigned char*)compressed,
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raw->CSQ_length);
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if (comp_status != Z_OK)
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ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
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for (c=seq->SQ,i=0;i<seqlength;c++,i++)
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*c=toupper(*c);
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return seq;
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}
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/**
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* Open the sequences database (.sdx file)
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* @param prefix name of the database (radical without extension)
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* @param prefix name of the database (radical without extension)
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* @param index integer
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*
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* @return file object
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*
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* @return file object
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*/
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FILE *open_seqfile(const char *prefix,int32_t index)
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{
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@ -161,22 +168,22 @@ FILE *open_seqfile(const char *prefix,int32_t index)
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"%s_%03d.sdx",
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prefix,
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index);
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fprintf(stderr,"# Coucou %s\n",filename_buffer);
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if (filename_length >= 1024)
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ECOERROR(ECO_ASSERT_ERROR,"file name is too long");
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filename_buffer[filename_length]=0;
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input=open_ecorecorddb(filename_buffer,&seqcount,0);
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if (input)
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fprintf(stderr,"# Reading file %s containing %d sequences...\n",
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filename_buffer,
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seqcount);
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return input;
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}
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@ -186,38 +193,38 @@ ecoseq_t *ecoseq_iterator(const char *prefix)
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static int32_t current_file_idx = 1;
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static char current_prefix[1024];
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ecoseq_t *seq;
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if (prefix)
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{
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current_file_idx = 1;
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if (current_seq_file)
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fclose(current_seq_file);
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strncpy(current_prefix,prefix,1023);
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current_prefix[1024]=0;
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current_seq_file = open_seqfile(current_prefix,
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current_file_idx);
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if (!current_seq_file)
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return NULL;
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}
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seq = readnext_ecoseq(current_seq_file);
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if (!seq && feof(current_seq_file))
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{
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current_file_idx++;
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fclose(current_seq_file);
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current_seq_file = open_seqfile(current_prefix,
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current_file_idx);
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if (current_seq_file)
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seq = readnext_ecoseq(current_seq_file);
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}
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return seq;
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}
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}
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Block a user