test v0.1.0.1

pirl-unc · Aug 7, 2023 · ef70f09 · ef70f09
1 parent 1de729b
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diff --git a/.gitignore b/.gitignore
@@ -5,7 +5,7 @@ build/
 __pycache__/
 src/ace.egg-info/
 notebooks/*.pt
-examples/*.xlsx
+examples/outputs/*.xlsx
 *.pyc
 .coverage*
 *.DS_Store

diff --git a/examples/run_ace_deconvolve.sh b/examples/run_ace_deconvolve.sh
@@ -1,20 +1,47 @@
+echo "Deconvolution Example 1: Empirical (Pool ID)."
 ace deconvolve \
   --readout-file-type pool_id \
-  --readout-files 25peptides_5perpool_3x_pool-id_readout.xlsx \
-  --assignment-excel-file 25peptides_5perpool_3x_seqsim_sat-solver.xlsx \
+  --readout-files ../test/data/25peptides_5perpool_3x_pool-id_readout.xlsx \
+  --assignment-excel-file ../test/data/25peptides_5perpool_3x_noseqsim_sat-solver.xlsx \
   --min-spot-count 300 \
-  --output-excel-file 25peptides_5perpool_3x_pool-id_readout_deconvolved_empirical.xlsx
+  --output-excel-file outputs/25peptides_5perpool_3x_pool-id_readout_deconvolved_empirical.xlsx
 
+echo "Deconvolution Example 2: Expectation Maximization (Pool ID)."
 ace deconvolve \
   --readout-file-type pool_id \
-  --readout-files 25peptides_5perpool_3x_pool-id_readout.xlsx \
-  --assignment-excel-file 25peptides_5perpool_3x_seqsim_sat-solver.xlsx \
+  --readout-files ../test/data/25peptides_5perpool_3x_pool-id_readout.xlsx \
+  --assignment-excel-file ../test/data/25peptides_5perpool_3x_noseqsim_sat-solver.xlsx \
   --mode em \
-  --output-excel-file 25peptides_5perpool_3x_pool-id_readout_deconvolved_em.xlsx
+  --output-excel-file outputs/25peptides_5perpool_3x_pool-id_readout_deconvolved_em.xlsx
 
+echo "Deconvolution Example 3: LASSO (Pool ID)."
 ace deconvolve \
   --readout-file-type pool_id \
-  --readout-files 25peptides_5perpool_3x_pool-id_readout.xlsx \
-  --assignment-excel-file 25peptides_5perpool_3x_seqsim_sat-solver.xlsx \
+  --readout-files ../test/data/25peptides_5perpool_3x_pool-id_readout.xlsx \
+  --assignment-excel-file ../test/data/25peptides_5perpool_3x_noseqsim_sat-solver.xlsx \
   --mode lasso \
-  --output-excel-file 25peptides_5perpool_3x_pool-id_readout_deconvolved_lasso.xlsx
+  --output-excel-file outputs/25peptides_5perpool_3x_pool-id_readout_deconvolved_lasso.xlsx
+
+echo "Deconvolution Example 4: Empirical (AID Plate Reader)."
+ace deconvolve \
+  --readout-file-type aid_plate_reader \
+  --readout-files ../test/data/25peptides_5perpool_3x_aid-plate-reader_readout.xlsx \
+  --assignment-excel-file ../test/data/25peptides_5perpool_3x_noseqsim_sat-solver.xlsx \
+  --min-spot-count 300 \
+  --output-excel-file outputs/25peptides_5perpool_3x_aid-plate-reader_readout_deconvolved_empirical.xlsx
+
+echo "Deconvolution Example 5: Expectation Maximization (AID Plate Reader)."
+ace deconvolve \
+  --readout-file-type aid_plate_reader \
+  --readout-files ../test/data/25peptides_5perpool_3x_aid-plate-reader_readout.xlsx \
+  --assignment-excel-file ../test/data/25peptides_5perpool_3x_noseqsim_sat-solver.xlsx \
+  --mode em \
+  --output-excel-file outputs/25peptides_5perpool_3x_aid-plate-reader_readout_deconvolved_em.xlsx
+
+echo "Deconvolution Example 6: LASSO (AID Plate Reader)."
+ace deconvolve \
+  --readout-file-type aid_plate_reader \
+  --readout-files ../test/data/25peptides_5perpool_3x_aid-plate-reader_readout.xlsx \
+  --assignment-excel-file ../test/data/25peptides_5perpool_3x_noseqsim_sat-solver.xlsx \
+  --mode lasso \
+  --output-excel-file outputs/25peptides_5perpool_3x_aid-plate-reader_readout_deconvolved_lasso.xlsx
diff --git a/examples/run_ace_generate.sh b/examples/run_ace_generate.sh
@@ -1,158 +1,156 @@
-echo "Example 1. Golfy without peptide sequences (120/12/3x)"
+# Golfy
+echo "Golfy Example 1: 90 Peptides, 9 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 120 \
-  --num-peptides-per-pool 12 \
+  --num-peptides 90 \
+  --num-peptides-per-pool 9 \
   --num-coverage 3 \
   --mode golfy \
-  --output-excel-file 120peptides_12perpool_3x_noseqsim_golfy.xlsx \
+  --output-excel-file outputs/90peptides_9perpool_3x_noseqsim_golfy.xlsx \
   --assign-well-ids 1 \
-  --num-plate-wells 96
-echo ""
+  --num-plate-wells 96 \
 
-echo "Example 2. SAT solver without peptide sequences (120/12/3x)"
+echo "Golfy Example 2: 100 Peptides, 5 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 120 \
-  --num-peptides-per-pool 12 \
+  --num-peptides 100 \
+  --num-peptides-per-pool 5 \
   --num-coverage 3 \
-  --cpsat-solver-num-processes 6 \
-  --mode cpsat_solver \
-  --output-excel-file 120peptides_12perpool_3x_noseqsim_sat-solver.xlsx \
+  --mode golfy \
+  --output-excel-file outputs/100peptides_5perpool_3x_noseqsim_golfy.xlsx \
   --assign-well-ids 1 \
-  --num-plate-wells 96
-echo ""
+  --num-plate-wells 96 \
 
-echo "Example 3. Golfy solver without peptide sequences (100/5/3x)"
+echo "Golfy Example 3: 120 Peptides, 8 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 100 \
-  --num-peptides-per-pool 5 \
+  --num-peptides 120 \
+  --num-peptides-per-pool 8 \
   --num-coverage 3 \
   --mode golfy \
-  --output-excel-file 100peptides_5perpool_3x_noseqsim_golfy.xlsx \
+  --output-excel-file outputs/120peptides_8perpool_3x_noseqsim_golfy.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo ""
 
-echo "Example 4. SAT solver without peptide sequences (100/5/3x)"
+echo "Golfy Example 4: 120 Peptides, 12 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 100 \
-  --num-peptides-per-pool 5 \
+  --num-peptides 120 \
+  --num-peptides-per-pool 12 \
   --num-coverage 3 \
-  --cpsat-solver-num-processes 6 \
-  --mode cpsat_solver \
-  --output-excel-file 100peptides_5perpool_3x_noseqsim_sat-solver.xlsx \
+  --mode golfy \
+  --output-excel-file outputs/120peptides_12perpool_3x_noseqsim_golfy.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo ""
 
-echo "Example 5. Golfy without peptide sequences (120/8/3x)"
+echo "Golfy Example 5: 220 Peptides, 11 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 120 \
-  --num-peptides-per-pool 8 \
+  --num-peptides 220 \
+  --num-peptides-per-pool 11 \
   --num-coverage 3 \
   --mode golfy \
-  --output-excel-file 120peptides_8perpool_3x_noseqsim_golfy.xlsx \
+  --output-excel-file outputs/220peptides_11perpool_3x_noseqsim_golfy.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo ""
 
-echo "Example 6. SAT solver without peptide sequences (120/8/3x)"
+echo "Golfy Example 6: 240 Peptides, 12 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 120 \
-  --num-peptides-per-pool 8 \
+  --num-peptides 240 \
+  --num-peptides-per-pool 12 \
   --num-coverage 3 \
-  --cpsat-solver-num-processes 6 \
-  --cpsat-solver-max-peptides-per-block 64 \
-  --mode cpsat_solver \
-  --output-excel-file 120peptides_8perpool_3x_noseqsim_sat-solver.xlsx \
+  --mode golfy \
+  --output-excel-file outputs/240peptides_12perpool_3x_noseqsim_golfy.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo ""
 
-echo "Example 7. Golfy with peptide sequences (25/5/3x)"
+echo "Golfy Example 7: 400 Peptides, 5 Peptides per Pool, 3x Coverage."
 ace generate \
-  --peptides-excel-file ../test/data/25peptide_sequences.xlsx \
+  --num-peptides 400 \
   --num-peptides-per-pool 5 \
   --num-coverage 3 \
   --mode golfy \
-  --output-excel-file 25peptides_5perpool_3x_seqsim_golfy.xlsx
-echo ""
+  --output-excel-file outputs/240peptides_12perpool_3x_noseqsim_golfy_384plates.xlsx \
+  --assign-well-ids 1 \
+  --num-plate-wells 384
 
-echo "Example 8. SAT solver with peptide sequences (25/5/3x)"
+echo "Golfy Example 8: 25 Peptides, 5 Peptides per Pool, 3x Coverage (with Sequences)."
 ace generate \
   --peptides-excel-file ../test/data/25peptide_sequences.xlsx \
   --num-peptides-per-pool 5 \
   --num-coverage 3 \
-  --cpsat-solver-num-processes 6 \
-  --mode cpsat_solver \
-  --output-excel-file 25peptides_5perpool_3x_seqsim_sat-solver.xlsx
-echo ""
+  --mode golfy \
+  --output-excel-file outputs/25peptides_5perpool_3x_seqsim_golfy.xlsx
 
-echo "Example 9. Golfy without peptide sequences (90/9/3x)"
+# CP-SAT Solver
+echo "CP-SAT Solver Example 1: 90 Peptides, 9 Peptides per Pool, 3x Coverage."
 ace generate \
   --num-peptides 90 \
   --num-peptides-per-pool 9 \
   --num-coverage 3 \
-  --mode golfy \
-  --output-excel-file 90peptides_9perpool_3x_noseqsim_golfy.xlsx \
+  --cpsat-solver-num-processes 6 \
+  --mode cpsat_solver \
+  --output-excel-file outputs/90peptides_9perpool_3x_noseqsim_sat-solver.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo ""
 
-echo "Example 10. SAT solver without peptide sequences (90/9/3x)"
+echo "CP-SAT Solver Example 2: 100 Peptides, 5 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 90 \
-  --num-peptides-per-pool 9 \
+  --num-peptides 100 \
+  --num-peptides-per-pool 5 \
   --num-coverage 3 \
   --cpsat-solver-num-processes 6 \
   --mode cpsat_solver \
-  --output-excel-file 90peptides_9perpool_3x_noseqsim_sat-solver.xlsx \
+  --output-excel-file outputs/100peptides_5perpool_3x_noseqsim_sat-solver.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo ""
 
-echo "Example 11. Golfy without peptide sequences (220/11/3x)"
+echo "CP-SAT Solver Example 3: 120 Peptides, 12 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 220 \
-  --num-peptides-per-pool 11 \
+  --num-peptides 120 \
+  --num-peptides-per-pool 12 \
   --num-coverage 3 \
-  --mode golfy \
-  --output-excel-file 220peptides_11perpool_3x_noseqsim_golfy.xlsx \
+  --cpsat-solver-num-processes 6 \
+  --mode cpsat_solver \
+  --output-excel-file outputs/120peptides_12perpool_3x_noseqsim_sat-solver.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo ""
 
-echo "Example 12. SAT solver without peptide sequences (220/11/3x)"
+echo "CP-SAT Solver Example 4: 120 Peptides, 8 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 220 \
-  --num-peptides-per-pool 11 \
+  --num-peptides 120 \
+  --num-peptides-per-pool 8 \
   --num-coverage 3 \
   --cpsat-solver-num-processes 6 \
+  --cpsat-solver-max-peptides-per-block 64 \
   --mode cpsat_solver \
-  --output-excel-file 220peptides_11perpool_3x_noseqsim_sat-solver.xlsx \
+  --output-excel-file outputs/120peptides_8perpool_3x_noseqsim_sat-solver.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo ""
 
-echo "Example 13. Golfy without peptide sequences (240/12/3x)"
+echo "CP-SAT Solver Example 5: 220 Peptides, 11 Peptides per Pool, 3x Coverage."
 ace generate \
-  --num-peptides 240 \
-  --num-peptides-per-pool 12 \
+  --num-peptides 220 \
+  --num-peptides-per-pool 11 \
   --num-coverage 3 \
-  --mode golfy \
-  --output-excel-file 240peptides_12perpool_3x_noseqsim_golfy.xlsx \
+  --cpsat-solver-num-processes 6 \
+  --mode cpsat_solver \
+  --output-excel-file outputs/220peptides_11perpool_3x_noseqsim_sat-solver.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
-echo""
 
-echo "Example 14. SAT solver without peptide sequences (240/12/3x)"
+echo "CP-SAT Solver Example 6: 240 Peptides, 12 Peptides per Pool, 3x Coverage."
 ace generate \
   --num-peptides 240 \
   --num-peptides-per-pool 12 \
   --num-coverage 3 \
   --cpsat-solver-num-processes 6 \
   --mode cpsat_solver \
-  --output-excel-file 240peptides_12perpool_3x_noseqsim_sat-solver.xlsx \
+  --output-excel-file outputs/240peptides_12perpool_3x_noseqsim_sat-solver.xlsx \
   --assign-well-ids 1 \
   --num-plate-wells 96
 echo""
 
+echo "CP-SAT Solver Example 7: 25 Peptides, 5 Peptides per Pool, 3x Coverage (with Sequences)."
+ace generate \
+  --peptides-excel-file ../test/data/25peptide_sequences.xlsx \
+  --num-peptides-per-pool 5 \
+  --num-coverage 3 \
+  --cpsat-solver-num-processes 6 \
+  --mode cpsat_solver \
+  --output-excel-file outputs/25peptides_5perpool_3x_seqsim_sat-solver.xlsx
diff --git a/examples/test.sh b/examples/test.sh
diff --git a/pyproject.toml b/pyproject.toml
@@ -26,7 +26,7 @@ requires = [
 
 [project]
 name = "ace"
-version = "0.1.0.0"
+version = "0.1.0.1"
 requires-python = ">=3.7"
 keywords = [
     "elispot",

diff --git a/src/acelib/block_assignment.py b/src/acelib/block_assignment.py
@@ -114,7 +114,7 @@ def get_96_well_ids():
             return ['%s%s' % (i[0], i[1]) for i in list(product(row_prefixes, col_prefixes))]
         def get_384_well_ids():
             row_prefixes = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P']
-            col_prefixes = range(1, 15)
+            col_prefixes = range(1, 25)
             return ['%s%s' % (i[0], i[1]) for i in list(product(row_prefixes, col_prefixes))]
 
         curr_plate_id = 1
@@ -147,7 +147,7 @@ def get_384_well_ids():
                 curr_plate_id += 1
             curr_well_id = curr_well_ids[0]
             curr_well_ids.pop(0)
-            self.plate_ids['pool_id'] = (curr_plate_id, curr_well_id)
+            self.plate_ids[pool_id] = (curr_plate_id, curr_well_id)
 
     def get_peptide_sequence(self, peptide_id: PeptideId) -> PoolId:
         """
@@ -220,7 +220,9 @@ def to_dataframe(self) -> pd.DataFrame:
                     else:
                         data['plate_id'].append('')
                         data['well_id'].append('')
-        return pd.DataFrame(data)
+        df = pd.DataFrame(data)
+        df.sort_values(by=['peptide_id'], inplace=True)
+        return df
 
     def is_optimal(
             self,

diff --git a/src/acelib/cli/cli_generate.py b/src/acelib/cli/cli_generate.py
@@ -145,6 +145,14 @@ def add_ace_generate_arg_parser(sub_parsers):
         choices=SequenceSimilarityFunctions.ALL,
         help="Sequence similarity function (default: %s)." % GENERATE_SEQUENCE_SIMILARITY_FUNCTION
     )
+    parser_optional.add_argument(
+        "--cluster-peptides",
+        dest="cluster_peptides",
+        type=bool,
+        default=True,
+        required=False,
+        help="Cluster peptides if set to true (default: true)."
+    )
 
     parser_optional_golfy = parser.add_argument_group("optional arguments (applies when '--mode golfy')")
     parser_optional_golfy.add_argument(
@@ -272,10 +280,12 @@ def run_ace_generate_from_parsed_args(args):
     # Step 1. Load peptide data
     if args.peptides_excel_file is not None:
         peptides = convert_dataframe_to_peptides(df_peptides=pd.read_excel(args.peptides_excel_file))
+        cluster_peptides = args.cluster_peptides
     else:
         peptides = []
         for i in range(1, args.num_peptides + 1):
             peptides.append(('peptide_%i' % i, ''))
+        cluster_peptides = False
 
     # Step 2. Check input parameters
     if len(peptides) % args.num_peptides_per_pool != 0 and args.mode == GenerateModes.CPSAT_SOLVER:
@@ -288,6 +298,7 @@ def run_ace_generate_from_parsed_args(args):
         num_peptides_per_pool=args.num_peptides_per_pool,
         num_coverage=args.num_coverage,
         trained_model_file=resources.path('acelib.resources.models', 'trained_model5.pt'),
+        cluster_peptides=cluster_peptides,
         mode=args.mode,
         sequence_similarity_function=args.sequence_similarity_function,
         sequence_similarity_threshold=args.sequence_similarity_threshold,

diff --git a/src/acelib/deconvolution.py b/src/acelib/deconvolution.py
@@ -76,7 +76,9 @@ def to_dataframe(self):
             data['pool_ids'].append(';'.join([str(p) for p in pool_ids]))
             data['num_coverage'].append(len(pool_ids))
             data['deconvolution_result'].append(label)
-        return pd.DataFrame(data)
+        df = pd.DataFrame(data)
+        df.sort_values(by=['peptide_id'], inplace=True)
+        return df
 
 
 def convert_to_golfy_spotcounts(