added option to set the same seed for all replicates in readcount tables

config.yml

@@ -30,9 +30,10 @@ difference_ratio: "23:31:46" #Rate of substitution:insertion:deletion.
                           #For PacBio the default values is 6:50:54
                           #For Nanopore it is 23:31:46
 ##Replicate params
-sd_rep: 0 #Standard deviation for varying the number of reads per genome between replicates,
+sd_rep_reads: 0 #Standard deviation for varying the number of reads per genome between replicates,
               #if 0 keep the same number of reads per genome for each replicate
               #else vary the read number between replicates by sampling from a normal distribution
+same_dist_rep: False #If True all replicates have the same read distribution (for log-normal distribution)
 seed: 1 #Set this parameter to a fixed number so data from random number generators is reproducible
 
 #Assembly finder parameters

mess/scripts/simulate_reads.rules

@@ -37,7 +37,22 @@ def get_input_value(path):
             raise Exception(f'{lastcol} is not recognized as an input to simulate reads')
 
 
+def get_read_counts_seed(rep, rep2seed, general_seed):
+    """
+    Function that returns a seed for calculating read counts
+    By default each replicate has a unique seed
+    If the param same_dist_rep is True, return a single seed for all replicates
+    """
+    try:
+        same_dist_rep = config['same_dist_rep']
+        if same_dist_rep:
+            return general_seed
+    except KeyError:
+        return rep2seed[int(rep)]
+
+
 input_val = get_input_value(config['input_table_path'])
+
 rule create_read_counts_table:
     '''
     Rule for generating a table per sample with read counts for each genome 
@@ -48,7 +63,7 @@ rule create_read_counts_table:
     output: rc_table='readcounts-{community}-{rep}.tsv'
 
     params: value=input_val,
-            seed=lambda wildcards: seed_dic[int(wildcards.rep)]
+            seed=lambda wildcards: get_read_counts_seed(wildcards.rep, seed_dic, config['seed'])
 
     log: "logs/read_counts_table/{community}-{rep}.txt"