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

.cproject

@@ -0,0 +1,122 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?fileVersion 4.0.0?>
+
+<cproject>
+<storageModule moduleId="org.eclipse.cdt.core.settings">
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+</extensions>
+</storageModule>
+<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+<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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+<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
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+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
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+</profile>
+</storageModule>
+<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
+</cconfiguration>
+</storageModule>
+<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+<project id="ecoPCR.null.1320766773" name="ecoPCR"/>
+</storageModule>
+</cproject>

.project

@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ecoPCR</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
+			<triggers>clean,full,incremental,</triggers>
+			<arguments>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
+					<value>all</value>
+				</dictionary>
+				<dictionary>
+					<key>?name?</key>
+					<value></value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
+					<value>false</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableFullBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
+					<value>clean</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.append_environment</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.contents</key>
+					<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildArguments</key>
+					<value></value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildCommand</key>
+					<value>make</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
+					<value>all</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.stopOnError</key>
+					<value>true</value>
+				</dictionary>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.cdt.core.cnature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

.pydevproject

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse-pydev version="1.0"?>
+
+<pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.4</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
+</pydev_project>

src/libecoPCR/ecoseq.c

@@ -4,6 +4,7 @@
 #include <zlib.h>
 #include <string.h>
 #include <stdio.h>
+#include <ctype.h>
 
 static FILE *open_seqfile(const char *prefix,int32_t index);
 
@@ -11,32 +12,32 @@ static FILE *open_seqfile(const char *prefix,int32_t index);
 ecoseq_t *new_ecoseq()
 {
 	void *tmp;
-	
+
 	tmp = ECOMALLOC(sizeof(ecoseq_t),"Allocate new ecoseq structure");
-	
+
 	return tmp;
 }
 
 int32_t delete_ecoseq(ecoseq_t * seq)
 {
-	
+
 	if (seq)
 	{
 		if (seq->AC)
 			ECOFREE(seq->AC,"Free sequence AC");
-			
+
 		if (seq->DE)
 			ECOFREE(seq->DE,"Free sequence DE");
-			
+
 		if (seq->SQ)
 			ECOFREE(seq->SQ,"Free sequence SQ");
-			
+
 		ECOFREE(seq,"Free sequence structure");
-		
+
 		return 0;
-			
+
 	}
-	
+
 	return 1;
 }
 
@@ -49,9 +50,9 @@ ecoseq_t *new_ecoseq_with_data( char *AC,
 	ecoseq_t *tmp;
 	int32_t lstr;
 	tmp = new_ecoseq();
-	
+
 	tmp->taxid=taxid_idx;
-	
+
 	if (AC)
 		{
 			lstr =strlen(AC);
@@ -97,12 +98,14 @@ ecoseq_t *readnext_ecoseq(FILE *f)
 	int32_t  comp_status;
 	unsigned long int seqlength;
 	int32_t  rs;
-	
+	char *c;
+	int32_t i;
+
 	raw = read_ecorecord(f,&rs);
-	
+
 	if (!raw)
 		return NULL;
-		
+
 	if (is_big_endian())
 	{
 		raw->CSQ_length = swap_int32_t(raw->CSQ_length);
@@ -110,44 +113,48 @@ ecoseq_t *readnext_ecoseq(FILE *f)
 		raw->SQ_length  = swap_int32_t(raw->SQ_length);
 		raw->taxid      = swap_int32_t(raw->taxid);
 	}
-	
+
 	seq = new_ecoseq();
-	
+
 	seq->taxid = raw->taxid;
-	
+
     seq->AC    = ECOMALLOC(strlen(raw->AC) +1,
                            "Allocate Sequence Accesion number");
     strncpy(seq->AC,raw->AC,strlen(raw->AC));
 
-                           
+
     seq->DE    = ECOMALLOC(raw->DE_length+1,
                            "Allocate Sequence definition");
     strncpy(seq->DE,raw->data,raw->DE_length);
-    
+
 	seqlength = seq->SQ_length = raw->SQ_length;
-    
+
     compressed = raw->data + raw->DE_length;
 
     seq->SQ = ECOMALLOC(seqlength+1,
                         "Allocate sequence buffer");
-                        
+
     comp_status = uncompress((unsigned char*)seq->SQ,
                              &seqlength,
                              (unsigned char*)compressed,
                              raw->CSQ_length);
-    
+
     if (comp_status != Z_OK)
     	ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
-    
+
+    for (c=seq->SQ,i=0;i<seqlength;c++,i++)
+    	*c=toupper(*c);
+
+
 	return seq;
 }
 
 /**
  * Open the sequences database (.sdx file)
- * @param	prefix	name of the database (radical without extension) 
+ * @param	prefix	name of the database (radical without extension)
  * @param	index 	integer
- * 
+ *
- * @return	file object 
+ * @return	file object
  */
 FILE *open_seqfile(const char *prefix,int32_t index)
 {
@@ -161,22 +168,22 @@ FILE *open_seqfile(const char *prefix,int32_t index)
 	                           "%s_%03d.sdx",
 	                           prefix,
 	                           index);
-	                           
+
 			fprintf(stderr,"# Coucou %s\n",filename_buffer);
-	                           
+
 
 	if (filename_length >= 1024)
 		ECOERROR(ECO_ASSERT_ERROR,"file name is too long");
 
 	filename_buffer[filename_length]=0;
-		
+
 	input=open_ecorecorddb(filename_buffer,&seqcount,0);
-	
+
 	if (input)
 		fprintf(stderr,"# Reading file %s containing %d sequences...\n",
 				filename_buffer,
 				seqcount);
-				
+
 	return input;
 }
 
@@ -186,38 +193,38 @@ ecoseq_t *ecoseq_iterator(const char *prefix)
 	static int32_t current_file_idx = 1;
 	static char    current_prefix[1024];
 	ecoseq_t       *seq;
-	
+
 	if (prefix)
 	{
 		current_file_idx = 1;
 
 		if (current_seq_file)
 			fclose(current_seq_file);
-			
+
 		strncpy(current_prefix,prefix,1023);
 		current_prefix[1024]=0;
-		
+
 		current_seq_file = open_seqfile(current_prefix,
 		 							    current_file_idx);
-		
+
 		if (!current_seq_file)
 			return NULL;
-			
+
 	}
-	
+
 	seq = readnext_ecoseq(current_seq_file);
-	
+
 	if (!seq && feof(current_seq_file))
 	{
 		current_file_idx++;
 		fclose(current_seq_file);
 		current_seq_file = open_seqfile(current_prefix,
 		 							    current_file_idx);
-		 							    
+
-		
+
 		if (current_seq_file)
 			seq = readnext_ecoseq(current_seq_file);
 	}
-	
+
 	return seq;
-}
+}