Revised TODO items

ning-y · Sep 15, 2023 · be75d37 · be75d37
1 parent 095531d
commit be75d37
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Showing 6 changed files with 8 additions and 29 deletions.
diff --git a/TODO.md b/TODO.md
@@ -24,3 +24,8 @@
 - ~~read parameters from config file~~
 - Document masking, etc. - nuances that affect the pipeline performance.
 - https://github.com/hillerlab/make_lastz_chains/issues/20 - temp files location
+
+## Minor things
+
+- lastz_q parameter - figure out what stands for and whether it is needed
+- 
diff --git a/__temp_get_ucsc_tool.sh b/__temp_get_ucsc_tool.sh
diff --git a/make_chains.py b/make_chains.py
@@ -199,7 +199,7 @@ def cleanup(parameters: PipelineParameters, project_paths: ProjectPaths):
 def run_pipeline(args):
     # setup project dir, parameters and step manager
     start_time = dt.now()
-    # TODO: class to hold paths within the project
+
     step_executables = StepExecutables(SCRIPT_LOCATION)
     project_dir = OutputDirectoryManager(args).project_dir
     parameters = PipelineParameters(args)
@@ -227,11 +227,10 @@ def run_pipeline(args):
 
     # now execute steps
     step_manager.execute_steps(parameters, step_executables, project_paths)
-    # check result?
+    # finalise the run
     save_final_chain(parameters, project_paths)
     cleanup(parameters, project_paths)
     tot_runtime = dt.now() - start_time
-    # TODO: skip chains with negative scores or < min_score
     to_log(f"make_lastz_chains run done in {tot_runtime}")
 
 

diff --git a/steps_implementations/chain_run_bundle_substep.py b/steps_implementations/chain_run_bundle_substep.py
@@ -24,7 +24,6 @@ def bundle_files(args, chrom_size, input_files):
             to_log(f"\nConsider {chrom} {chrom_size[chrom]}")
 
         if f"{chrom}.psl" not in input_files:
-            # TODO: consider this when fixing cat step
             to_log(f"\t--> file {chrom}.psl does not exist. Next")
             continue
 

diff --git a/steps_implementations/chain_run_step.py b/steps_implementations/chain_run_step.py
@@ -52,7 +52,6 @@ def make_chains_joblist(project_paths: ProjectPaths,
     # Prepare parameters
     seq1_dir = params.seq_1_dir
     seq2_dir = params.seq_2_dir
-    # TODO: figure out what is this lastz_q parameter stands for
     # matrix = params.lastz_q if params.lastz_q else ""
     # matrix = ""
     min_score = params.chain_min_score

diff --git a/steps_implementations/clean_chain_step.py b/steps_implementations/clean_chain_step.py
@@ -27,7 +27,7 @@ def do_chains_clean(params: PipelineParameters,
 
     shutil.move(input_chain, project_paths.before_cleaning_chain)
     to_log(f"Chain to be cleaned saved to: {project_paths.before_cleaning_chain}")
-    # TODO: I don't really like this original decision, to be revised
+    # TODO: revise how the filenames are handled
     _output_chain = input_chain.removesuffix(".gz")
     _intermediate_chain = f"{_output_chain}__temp"
     _clean_chain_args = params.clean_chain_parameters.split()