Merge branch 'luke_tests'

python/obitools3/commands/import.pyx

@@ -106,7 +106,7 @@ def run(config):
         raise RuntimeError('No file format specified')
     
     # Temporary way to handle NA values
-    NA_list = ["nan"]
+    #NA_list = ["nan"]
     
     # Create DMS
     d = OBIDMS(config['obi']['defaultdms'])
@@ -126,10 +126,11 @@ def run(config):
             view[i][tag] = seq['tags'][tag]
         i+=1
 
-    print(view)
+   #print(view)
-   # print(view.__repr__())
+    print(view.__repr__())
 
     view.save_and_close()
     d.close()
     
+    print("Done.")
         

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -1,5 +1,3 @@
-../../../src/obidmscolumn_bool.c
-../../../src/obidmscolumn_bool.h
 ../../../src/bloom.h
 ../../../src/bloom.c
 ../../../src/char_str_indexer.h
@@ -39,3 +37,15 @@
 ../../../src/obiview.c
 ../../../src/utils.h
 ../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -1,5 +1,3 @@
-../../../src/obidmscolumn_char.c
-../../../src/obidmscolumn_char.h
 ../../../src/bloom.h
 ../../../src/bloom.c
 ../../../src/char_str_indexer.h
@@ -39,3 +37,15 @@
 ../../../src/obiview.c
 ../../../src/utils.h
 ../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -1,9 +1,7 @@
-../../../src/obidmscolumn_float.c
-../../../src/obidmscolumn_float.h
-../../../src/char_str_indexer.h
-../../../src/char_str_indexer.c
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h
@@ -39,3 +37,15 @@
 ../../../src/obiview.c
 ../../../src/utils.h
 ../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -1,9 +1,7 @@
-../../../src/obidmscolumn_int.c
-../../../src/obidmscolumn_int.h
-../../../src/char_str_indexer.h
-../../../src/char_str_indexer.c
 ../../../src/bloom.h
 ../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
 ../../../src/crc64.h
 ../../../src/crc64.c
 ../../../src/dna_seq_indexer.h
@@ -39,3 +37,15 @@
 ../../../src/obiview.c
 ../../../src/utils.h
 ../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -1,5 +1,3 @@
-../../../src/obidmscolumn_seq.c
-../../../src/obidmscolumn_seq.h
 ../../../src/bloom.h
 ../../../src/bloom.c
 ../../../src/char_str_indexer.h
@@ -39,3 +37,15 @@
 ../../../src/obiview.c
 ../../../src/utils.h
 ../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -1,5 +1,3 @@
-../../../src/obidmscolumn_str.c
-../../../src/obidmscolumn_str.h
 ../../../src/bloom.h
 ../../../src/bloom.c
 ../../../src/char_str_indexer.h
@@ -39,3 +37,15 @@
 ../../../src/obiview.c
 ../../../src/utils.h
 ../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obiseq.cfiles

@@ -37,3 +37,15 @@
 ../../../src/obiview.c
 ../../../src/utils.h
 ../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obitaxo.cfiles

@@ -37,3 +37,15 @@
 ../../../src/obiview.c
 ../../../src/utils.h
 ../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obigrep.py

@@ -0,0 +1,51 @@
+import sys
+import argparse
+
+from obitools3.obidms._obidms import OBIDMS
+
+if __name__ == '__main__': 
+    
+    parser = argparse.ArgumentParser(description='Pseudo obigrep.')
+    
+    parser.add_argument('-V', '--view', dest='view', type=str,
+                       help='Name of the view that should be considered')    
+
+    parser.add_argument('-N', '--new_view', dest='new_view', type=str,
+                       help='Name of the new view that should be created')    
+    
+#     parser.add_argument('-k', '--key', dest='key', type=str,
+#                        help='Name of the key that should be considered')
+# 
+#     parser.add_argument('-c', '--comp', dest='comparison', type=int,
+#                        help='Comparison to be made: -1:< ; 0:== ; 1:>')
+# 
+#     parser.add_argument('-v', '--value', dest='value', type=object,
+#                        help='Value to be compared')
+
+    args = parser.parse_args()
+    
+    d = OBIDMS('tdms')
+    
+    #condition = 1
+    line_selec = []
+    
+    v = d.open_view(args.view)
+    
+    i = 0
+    for l in v :
+        if l['score'] > 350 : 
+            line_selec.append(i)
+        i+=1
+        
+    new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obigrep "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
+
+    print("\n")
+    print(new_v.__repr__())
+
+    v.save_and_close()
+    new_v.save_and_close()
+    
+    d.close()
+
+    print("\nDone.")
+    

python/obitools3/obihead.py

@@ -0,0 +1,43 @@
+import sys
+import argparse
+
+from obitools3.obidms._obidms import OBIDMS
+
+if __name__ == '__main__': 
+    
+    parser = argparse.ArgumentParser(description='Pseudo obihead.')
+    
+    parser.add_argument('-V', '--view', dest='view', type=str,
+                       help='Name of the view that should be considered')    
+
+    parser.add_argument('-N', '--new_view', dest='new_view', type=str,
+                       help='Name of the new view that should be created')    
+    
+    parser.add_argument('-n', '--nb', dest='nb_lines', type=int,
+                       help='Number of lines that should be taken')    
+    
+
+    args = parser.parse_args()
+    
+    d = OBIDMS('tdms')
+    
+    #condition = 1
+    line_selec = []
+    
+    v = d.open_view(args.view)
+    
+    for i in range(0, args.nb_lines) :
+        line_selec.append(i)
+        
+    new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obihead "+str(args.nb_lines)+", "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
+
+    print("\n")
+    print(new_v.__repr__())
+
+    v.save_and_close()
+    new_v.save_and_close()
+    
+    d.close()
+
+    print("\nDone.")
+    

src/bloom.c

@@ -26,9 +26,9 @@
 #define MAKESTRING(n) STRING(n)
 #define STRING(n) #n
 
-#ifdef __linux__
+//#ifdef __linux__										// TODO commented because triggers error on luke21
-unsigned detect_bucket_size(unsigned fallback_size);
+//unsigned detect_bucket_size(unsigned fallback_size);
-#endif
+//#endif
 
 
 static int test_bit_set_bit(unsigned char * buf, unsigned int x, int set_bit)
@@ -89,11 +89,11 @@ static void setup_buckets(struct bloom * bloom, unsigned int cache_size)
   // either compute it or use built-in default
 
   if (cache_size == 0) {
-#ifdef __linux__
+//#ifdef __linux__													// TODO commented because triggers error on luke21
-    cache_size = detect_bucket_size(BLOOM_BUCKET_SIZE_FALLBACK);
+//    cache_size = detect_bucket_size(BLOOM_BUCKET_SIZE_FALLBACK);
-#else
+//#else
     cache_size = BLOOM_BUCKET_SIZE_FALLBACK;
-#endif
+//#endif
   }
 
   bloom->buckets = (bloom->bytes / cache_size);

src/obidmscolumn.c

@@ -587,7 +587,9 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	}
 
 	// Build the indexer name if needed
-	if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (strcmp(indexer_name, "") == 0))
+	if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
+	{
+		if (strcmp(indexer_name, "") == 0)
 		{
 			final_indexer_name = obi_build_indexer_name(column_name, version_number);
 			if (final_indexer_name == NULL)
@@ -598,6 +600,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 			final_indexer_name = (char*) malloc((strlen(indexer_name)+1)*sizeof(char));
 			strcpy(final_indexer_name, indexer_name);
 		}
+	}
 
 	returned_data_type = data_type;
 	if ((data_type == OBI_STR) || (data_type == OBI_SEQ))