predict chip dict working

pyproject.toml

@@ -35,7 +35,8 @@ dependencies = [
     "snakemake >= 8",
     "pandas",
     "thefuzz",
-    "pyyaml >= 5.1",
+#    "pyyaml >= 5.1",
+    "ruamel.yaml",
     "snakemake-executor-plugin-cluster-generic >= 1.0.9",
     "graphviz"
 ]

snakePipes/common_functions.py

@@ -5,7 +5,8 @@
 import subprocess
 import os
 import re
-import yaml
+#import yaml
+from ruamel.yaml import YAML
 import glob
 import sys
 import shutil
@@ -88,8 +89,10 @@ def namesOKinR(sampleNames):
 
 
 def load_configfile(configFiles, verbose, info='Config'):
+    yaml=YAML(typ='safe')
     with open(configFiles, "r") as f:
-        config = yaml.load(f, Loader=yaml.FullLoader)
+        #config = yaml.load(f, Loader=yaml.FullLoader)
+        config = yaml.load(f)
 
     config = sanity_dict_clean(config)
 
@@ -102,9 +105,15 @@ def load_configfile(configFiles, verbose, info='Config'):
     return config
 
 
-def write_configfile(configFile, config):
+def write_configfile(configFile, config, trafo):
+    yaml=YAML(typ='safe')
+    yaml.default_flow_style = False
     with open(configFile, 'w') as f:
-        yaml.dump(config, f, default_flow_style=False)
+        #yaml.dump(config, f, default_flow_style=False)
+        if trafo:
+            yaml.dump(config, f, transform=trafo)
+        else:
+            yaml.dump(config, f)
 
 
 # returns all key-value pairs that are different from dict1 to dict2
@@ -632,7 +641,7 @@ def commonYAMLandLogs(baseDir, workflowDir, defaults, args, callingScript):
     # save to configs.yaml in outdir
     config = defaults
     config.update(vars(args))  # This allows modifications of args after handling a user config file to still make it to the YAML given to snakemake!
-    write_configfile(os.path.join(args.outdir, '{}.config.yaml'.format(workflowName)), config)
+    write_configfile(os.path.join(args.outdir, '{}.config.yaml'.format(workflowName)), config, trafo=None)
 
     # merge cluster config files: 1) global one, 2) workflow specific one, 3) user provided one
     cfg = load_configfile(os.path.join(baseDir, "shared", "defaults.yaml"), False, "defaults")
@@ -719,7 +728,7 @@ def print_DAG(args, snakemake_cmd, callingScript, defaults):
         config['verbose'] = False
         write_configfile(
             os.path.join(args.outdir,
-                         '{}.config.yaml'.format(workflowName)), config)
+                         '{}.config.yaml'.format(workflowName)), config, trafo=None)
 
         DAGproc = subprocess.Popen(
             snakemake_cmd + " --rulegraph -q ",
@@ -734,7 +743,7 @@ def print_DAG(args, snakemake_cmd, callingScript, defaults):
         config['verbose'] = oldVerbose
         write_configfile(
             os.path.join(args.outdir, '{}.config.yaml'.format(workflowName)),
-            config)
+            config, trafo=None)
 
 
 def logAndExport(args, workflowName):
@@ -794,6 +803,9 @@ def runAndCleanup(args, cmd, logfile_name):
     if args.emailAddress:
        sendEmail(args, 0)
 
+def tr(s):
+    return s.replace('null', 'None')
+
 
 def predict_chip_dict(wdir, input_pattern_str, bamExt, fromBAM=None):
     """
@@ -856,14 +868,14 @@ def predict_chip_dict(wdir, input_pattern_str, bamExt, fromBAM=None):
             print("No control sample found!")
 
         chip_dict_pred["chip_dict"][i] = {}
-        chip_dict_pred["chip_dict"][i]['Control'] = tmp if tmp != "" else None
+        chip_dict_pred["chip_dict"][i]['Control'] = tmp if tmp !=  "" else None
         if re.match(".*(H3K4me1|H3K36me3|H3K9me3|H3K27me3).*", i, re.IGNORECASE):
             chip_dict_pred["chip_dict"][i]['Broad'] = True
         else:
             chip_dict_pred["chip_dict"][i]['Broad'] = False
 
     outfile = os.path.join(wdir, "chip_seq_sample_config.PREDICTED.yaml")
-    write_configfile(outfile, chip_dict_pred)
+    write_configfile(outfile, chip_dict_pred,trafo=tr)
     print("---------------------------------------------------------------------------------------")
     print("ChIPseq sample configuration is written to file ", outfile)
     print("Please check and modify this file - this is just a guess! Then run the workflow with it.")

snakePipes/snakePipes.py

@@ -414,15 +414,15 @@ def updateConfig(args):
         else:
             sys.exit("Config file not found\n")
     updatedDict = cof.merge_dicts(currentDict, d)
-    cof.write_configfile(os.path.join(baseDir, "shared", "defaults.yaml"), updatedDict)
+    cof.write_configfile(os.path.join(baseDir, "shared", "defaults.yaml"), updatedDict, trafo=None)
 
     #update conda-prefix in snakemakeProfile
     if args.condaEnvDir:
         profilePath = cof.resolveSnakemakeProfile(d['snakemakeProfile'], baseDir)
         f = open(profilePath / 'config.yaml')
         pf = yaml.load(f, Loader=yaml.FullLoader)
         pf['conda-prefix'] = args.condaEnvDir
-        cof.write_configfile(os.path.join(profilePath, "config.yaml"), pf)
+        cof.write_configfile(os.path.join(profilePath, "config.yaml"), pf, trafo=None)
         f.close()
 
     cof.load_configfile(

snakePipes/workflows/ChIPseq/internals.snakefile

@@ -104,7 +104,7 @@ with open(samples_config, "r") as f:
         exit(1)
     del chip_dict_tmp
 
-cf.write_configfile(os.path.join("chip_samples.yaml"), chip_dict)
+cf.write_configfile(os.path.join("chip_samples.yaml"), chip_dict, trafo=None)
 
 # create unique sets of control samples, ChIP samples with and without control
 control_samples = set()