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Merge branch 'luke_tests'

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This commit is contained in:
Celine Mercier
2016-04-28 11:17:24 +02:00
parent 6ea2cfb9ca 0eca86107e
commit b3976fa461
13 changed files with 218 additions and 36 deletions
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9
python/obitools3/commands/import.pyx
View File

@ -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.__repr__())
#print(view)
print(view.__repr__())
view.save_and_close()
d.close()
print("Done.")

14
python/obitools3/obidms/_obidmscolumn_bool.cfiles
View File

@ -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

14
python/obitools3/obidms/_obidmscolumn_char.cfiles
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@ -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

18
python/obitools3/obidms/_obidmscolumn_float.cfiles
View File

@ -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

18
python/obitools3/obidms/_obidmscolumn_int.cfiles
View File

@ -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

14
python/obitools3/obidms/_obidmscolumn_seq.cfiles
View File

@ -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

14
python/obitools3/obidms/_obidmscolumn_str.cfiles
View File

@ -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

12
python/obitools3/obidms/_obiseq.cfiles
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@ -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

12
python/obitools3/obidms/_obitaxo.cfiles
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@ -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

51
python/obitools3/obigrep.py Normal file
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@ -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.")

43
python/obitools3/obihead.py Normal file
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@ -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.")

14
src/bloom.c
View File

@ -26,9 +26,9 @@
#define MAKESTRING(n) STRING(n)
#define STRING(n) #n
#ifdef __linux__
unsigned detect_bucket_size(unsigned fallback_size);
#endif
//#ifdef __linux__ // TODO commented because triggers error on luke21
//unsigned detect_bucket_size(unsigned fallback_size);
//#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__
cache_size = detect_bucket_size(BLOOM_BUCKET_SIZE_FALLBACK);
#else
//#ifdef __linux__ // TODO commented because triggers error on luke21
// cache_size = detect_bucket_size(BLOOM_BUCKET_SIZE_FALLBACK);
//#else
cache_size = BLOOM_BUCKET_SIZE_FALLBACK;
#endif
//#endif
}
bloom->buckets = (bloom->bytes / cache_size);

21
src/obidmscolumn.c
View File

@ -587,16 +587,19 @@ 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))
{
final_indexer_name = obi_build_indexer_name(column_name, version_number);
if (final_indexer_name == NULL)
return NULL;
}
else
{
final_indexer_name = (char*) malloc((strlen(indexer_name)+1)*sizeof(char));
strcpy(final_indexer_name, indexer_name);
if (strcmp(indexer_name, "") == 0)
{
final_indexer_name = obi_build_indexer_name(column_name, version_number);
if (final_indexer_name == NULL)
return NULL;
}
else
{
final_indexer_name = (char*) malloc((strlen(indexer_name)+1)*sizeof(char));
strcpy(final_indexer_name, indexer_name);
}
}
returned_data_type = data_type;