diff --git a/_modules/GPU_chunkMapper.py b/_modules/GPU_chunkMapper.py
index ea97637904e594f3557da3de9c4e3e9ee2c02760..ba3d3429ca5508bf3e7dcb14df02d354c1cb7827 100644
--- a/_modules/GPU_chunkMapper.py
+++ b/_modules/GPU_chunkMapper.py
@@ -35,6 +35,11 @@ class GPU_chunkMapper(gpuBasicMapper):
max_nb_occ = getMaxNbOccPerSeq(o_nb_occ_foreach_extract_in_seqs, chunk_size, 1)
ficname1 = "read_occ_positions" + str(idx_seq) + "_" + str(chunk_idx)
ficname2 = "reduced" + str(idx_seq) + "_" + str(chunk_idx)
+ ficname3 = "max_occ" + str(idx_seq) + "_" + str(chunk_idx)
+ fname=os.path.join(self.ficdir, ficname3)
+ of = open(fname,"w")
+ of.write(str(max_nb_occ))
+ of.close()
if (max_nb_occ>0):
host_read_occ_positions = self.getOccPositions(max_nb_occ, 1, chunk_size)
# Gets reduced version of output_reads_nb_occ_in_seqs that enables me to iterate only on useful elements
@@ -66,9 +71,6 @@ class GPU_chunkMapper(gpuBasicMapper):
for seq in self.seq_data.refseq_list:
h = nb_extracts // self.nb_chunks # TODO: change code here to take nb_chunks into account.
extracts_chunk = extracts_l[0:h+1] # Problem here: element at index h is not copied
- # print extracts_chunk
- # print len(extracts_chunk)
- # print "h=",h," extcats_chunk[h]=",extracts_chunk[h]
self.mapOneChunk(extracts_chunk,h+1,0, seq,seq_sizes_l[idx_seq], idx_seq)
extracts_chunk=extracts_l[h+1:]
self.mapOneChunk(extracts_chunk,nb_extracts-h-1, 1, seq, seq_sizes_l[idx_seq], idx_seq)
diff --git a/_modules/GPU_mapper.py b/_modules/GPU_mapper.py
index 7139d3b16013cf8f10f91d14edcdb0f34aa78348..959be62ea81d832d04b6044b580f9d8882743618 100644
--- a/_modules/GPU_mapper.py
+++ b/_modules/GPU_mapper.py
@@ -36,6 +36,18 @@ class gpuBasicMappingResultsForCov:
self.rev_cpl_PE2_start_match=l_matches[3]
self.rev_cpl_PE2_stop_match=l_matches[4]
+def getGPUMappingResults(reduced_fic,occ_pos_fic,max_nb_occ_fic,nb_reads,nb_extracts,ref_data,single=True):
+ reduced=np.loadtxt(reduced_fic, dtype=np.int64, delimiter='|')
+ occ_pos=np.loadtxt(occ_pos_fic, dtype=np.int32, delimiter='|')
+ f_nb_occ = open(max_nb_occ_fic)
+ str_nb_occ = f_nb_occ.read()
+ f_nb_occ.close()
+ max_nb_occ = int(str_nb_occ)
+ mres=gpuBasicMappingResults(reduced, occ_pos, max_nb_occ, nb_reads,
+ nb_extracts, ref_data,single)
+ return mres
+
+
## Class to encapsulate the results of the mapping of all read extracts against all sequences.
class gpuBasicMappingResults:
## Constructor
@@ -142,7 +154,7 @@ class gpuBasicMapper:
def __init__(self,read_extracts,ref_data):
self.read_extracts=read_extracts
self.seq_data=ref_data
- self.starting_from=0
+ #self.starting_from=0
## Prepare input parameters on device side, only available for parameters that are used by several kernels.
def prepInputOnDevice(self,input_rextracts,nb_sequences,nb_extracts):
diff --git a/_modules/functions_PhageTerm_gpu.py b/_modules/functions_PhageTerm_gpu.py
index 8ecd329ada96d8666be93260f43c9a885381bf36..2e13729e69ab40f1d42f73428ca89a4d4ada6304 100644
--- a/_modules/functions_PhageTerm_gpu.py
+++ b/_modules/functions_PhageTerm_gpu.py
@@ -8,6 +8,10 @@ import numpy as np
from IData_handling import ReadGetter
from utilities import reverseComplement,hybridCoverage,correctEdge
+##
+# This function aims at processing the results of the mapping performed on GPU but partilly (a part of the reads against a part of a sequence).
+def readsCoverageGPU_partial(id_seq,id_chunk):
+ pass
## Equivalent to the readsCoverage function
#
diff --git a/tests/test_GPUMapper.py b/tests/test_GPUMapper.py
index a698d7b19ad010f6f26c0f33ebf4b61a22722832..7f54680ee745109810a2b143d78a4ef0bdbaa587 100644
--- a/tests/test_GPUMapper.py
+++ b/tests/test_GPUMapper.py
@@ -10,6 +10,7 @@ import sys
sys.path.append("..")
from _modules.GPU_chunkMapper import GPU_chunkMapper
+from _modules.GPU_mapper import getGPUMappingResults
from _modules.IData_handling import refData,readsExtractsS
from data_refseq import refseq_list
@@ -41,20 +42,7 @@ class TestGPUMapper (unittest.TestCase):
re.nb_extracts=nb_extracts
re.nb_reads=16895
mapper=GPU_chunkMapper(re,rd,ficdir,2)
- # print "nb extracts=",re.nb_extracts
- # print "re.nb_extracts//2=",re.nb_extracts//2
- print all_extracts_l[33790]
- # print all_extracts_l[33791]
- #print all_extracts_l
- # print all_extracts_l[11104] # appears once in seq 0
- # print all_extracts_l[11105] # appears 1 in seq 0
- # print all_extracts_l[11106] # does not appear
- # print all_extracts_l[11107] # does not appear
- #
- # print all_extracts_l[60000] # does not appear
- # print all_extracts_l[60001] # does not appear
- # print all_extracts_l[60002] # appears in seq3
- #print all_extracts_l[
+ #print all_extracts_l[33790]
mapper.doMapping()
self.assertTrue(os.path.isfile(os.path.join(ficdir, "read_occ_positions0_0")))
self.assertTrue(os.path.isfile(os.path.join(ficdir, "read_occ_positions0_1")))
@@ -78,6 +66,17 @@ class TestGPUMapper (unittest.TestCase):
self.assertTrue(os.path.isfile(os.path.join(ficdir, "reduced4_0")))
self.assertTrue(os.path.isfile(os.path.join(ficdir, "reduced4_1")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ0_0")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ0_1")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ1_0")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ1_1")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ2_0")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ2_1")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ3_0")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ3_1")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ4_0")))
+ self.assertTrue(os.path.isfile(os.path.join(ficdir, "max_occ4_1")))
+
i_occ_pos = np.loadtxt(os.path.join(ficdir, "read_occ_positions0_0"), dtype=np.int32, delimiter='|')
self.assertEqual(i_occ_pos[7677],1864)
self.assertEqual(i_occ_pos[7678],1954)
@@ -106,6 +105,13 @@ class TestGPUMapper (unittest.TestCase):
self.assertTrue(found1)
self.assertTrue(found2)
+ f_nb_occ=open(os.path.join(ficdir,"max_occ0_0"))
+ str_nb_occ=f_nb_occ.read()
+ f_nb_occ.close()
+ max_nb_occ=int(str_nb_occ)
+ self.assertEqual(max_nb_occ,15690)
+
+
reduced = np.loadtxt(os.path.join(ficdir, "reduced2_0"), dtype=np.int64, delimiter='|')
found = False
i = 0
@@ -116,8 +122,8 @@ class TestGPUMapper (unittest.TestCase):
found=True
nb_occ=reduced[i+1]
i+=1
- #self.assertTrue(found)
- #self.assertEqual(nb_occ,2)
+ self.assertTrue(found)
+ self.assertEqual(nb_occ,2)
reduced = np.loadtxt(os.path.join(ficdir, "reduced2_1"), dtype=np.int64, delimiter='|')
found = False
@@ -134,6 +140,20 @@ class TestGPUMapper (unittest.TestCase):
def testIterationOverMappingResults(self):
+ rd = refData(refseq_list, 20, "")
+ re = readsExtractsS(20)
+ re.r_extracts_list = all_extracts_l
+ re.nb_extracts = nb_extracts
+ re.nb_reads = 16895
+ mapper = GPU_chunkMapper(re, rd, ficdir, 2)
+ mapper.doMapping()
+ mres=getGPUMappingResults(os.path.join(ficdir, "reduced3_1"), os.path.join(ficdir, "read_occ_positions3_1"),
+ os.path.join(ficdir,"max_occ3_1"), re.nb_reads, re.nb_extracts, rd, single=True)
+ for r, r_hostseq, idx_read in mres.mappingResultsForSeq(refseq_list[3]):
+ if (idx_read==6691):
+ self.assertEqual(r.)
+
+
pass
if __name__ == "__main__":