Merged commit of all releases to this date:

### First release for megSAP
- added support for straglr 1.5.0
- changed output folder structure to match ExpansionHunter/REViewer output

### Plot modification
- changed the output format of plots
- modified size of plots
- added pathogenic threshold in plots

### Bugfix: Deterministic Plots
- set a constant hashsalt (seed) to make SVG plot (node names) deterministic

### Bugfix: Fixed length calculation of wt/pathogenic threshold
- The length of pathogenic range and wildtype is now calculated based on the reference motif since the repeat unit length may change in straglr 1.5.1.

Author: leonschuetz

.gitignore

@@ -0,0 +1,5 @@
+.vscode
+.idea
+src/utils/__pycache__
+src/__pycache__
+src/utils/.vscode

src/straglron.py

@@ -8,6 +8,7 @@
 import utils.extract_repeats as extract_repeats
 import shutil
 
+
 def is_valid_file(parser, arg, type):
     """
     Check if the provided file exists and has a .bed or .tsv extension.
@@ -29,28 +30,28 @@ def is_valid_file(parser, arg, type):
             return arg
 
 
-#Argument parser for command line interface including necessary file and options
+# Argument parser for command line interface including necessary file and options
 
 parser = argparse.ArgumentParser()
 
-#These arguments are always required
+# These arguments are always required
 
 parser.add_argument("path_input_bed", type=lambda x: is_valid_file(parser, x, "bed"), help="Path to input bed file")
 parser.add_argument("path_input_tsv", type=lambda x: is_valid_file(parser, x, "tsv"), help="Path to input tsv file")
 parser.add_argument("loci_file", type=lambda x: is_valid_file(parser, x, "bed"), help="Path to Loci file used for straglr analysis")
 parser.add_argument("-o", "--output", type=str, required=True, help="Path to output folder")
 
-#These Arguments are optional and produce histograms for each locus and sort the output .txt file based on a normalized increase in repeats respectively
+# These Arguments are optional and produce histograms for each locus and sort the output .txt file based on a normalized increase in repeats respectively
 
 parser.add_argument("--hist", action="store_true", help="Plots histograms of pathogenic expansions")
 parser.add_argument("--score", action="store_true", help="Expansion in output file is sorted by normalized size difference score")
 
-#Activates new clustering method 
+# Activates new clustering method 
 
 parser.add_argument("--altclust", action="store_true", help="Uses Thomas Clustering")
 parser.add_argument("-c", "--cutoff", type=int, default=2, help="Sets number of reads cutoff when clustering unimodal or bimodal allele read frequencies")
 
-#These arguments are required for producing the allele length visualization 
+# These arguments are required for producing the allele length visualization 
 
 parser.add_argument("--alleles", action="store_true", help="Turns on the allele visualization")
 parser.add_argument("--bam", type=str, help="Location of Bam file of interest")
@@ -59,76 +60,63 @@ def is_valid_file(parser, arg, type):
 
 args = parser.parse_args()
 
+
 def outputWriter(output_expansion: "list[Expansion]", sample_id, args):
 
-    #Base output here
-    sample_folder_path = args.output + "/" + sample_id
-    result_file_path = sample_folder_path + "/" + sample_id + ".txt"
-    if not (os.path.exists(sample_folder_path)):
-        os.mkdir(sample_folder_path)
+    # Base output here
+    result_file_path = args.output + "/" + sample_id + ".tsv"
+    if not (os.path.exists(args.output)):
+        os.mkdir(args.output)
 
     with open(result_file_path, 'w') as f:
         print("Writing result file ...")
         f.write("#chr\tstart\tend\trepeat_id\trepeat_unit\tcopy_number\tsize\twt_size\tin_pathogenic_range\tsize_difference\tallele1_support\tallele2_support\tscore\n")
 
         if args.altclust:
-
             for x in output_expansion:
                 f.write("{}\t{}\t{}\t{}\t{:.1f}/{:.1f}\t{}/{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(x.chr, x.start, x.end, x.repeat_id, (x.new_allele1/len(x.repeat_unit)), (x.new_allele2/len(x.repeat_unit)), x.new_allele1, x.new_allele2, x.wt_size, x.new_in_pathogenic_range, x.new_size_difference, x.new_allele1_support, x.new_allele2_support,x.new_norm_score))
-
         else:
-
             for x in output_expansion:
                 f.write("{}\t{}\t{}\t{}\t{:.1f}/{:.1f}\t{}/{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(x.chr, x.start, x.end, x.repeat_id, (x.allele1_size/len(x.repeat_unit)), (x.allele2_size/len(x.repeat_unit)), x.allele1_size, x.allele2_size, x.wt_size, x.in_pathogenic_range, x.size_difference, x.allele1_support, x.allele2_support,x.norm_score))                
 
         print("Result file completed.")      
 
-    #Base output plus Histograms
+    # Base output plus Histograms
     if args.hist:
-        plot_folder_path = sample_folder_path + "/plots"
-
-        if(os.path.exists(plot_folder_path)):
-            shutil.rmtree(plot_folder_path)
-        os.mkdir(plot_folder_path)
-        
         print("Generating read distribution histograms ...")
 
         if args.altclust:
             for x in output_expansion:
-                vis.plotHistogram(x, plot_folder_path, args.altclust)
-                    
+                vis.plotHistogram(x, args.output, args.altclust)
         else:
             for x in output_expansion:
-                vis.plotHistogram(x, plot_folder_path, args.altclust)
+                vis.plotHistogram(x, args.output, args.altclust)
 
         print("Histograms completed.")
 
 
-    #Base with Allele Visualization
+    # Base with Allele Visualization
     if args.alleles:
-        repeats_fasta_folder = sample_folder_path + "/" + "repeats"
-
-        if(os.path.exists(repeats_fasta_folder)):
-            shutil.rmtree(repeats_fasta_folder)
-        os.mkdir(repeats_fasta_folder)
-
         print("Generating allele composition graphs ...")
 
         for x in output_expansion:    
-            extract_repeats.fastaMaker(args.path_input_tsv, x.chr + ":"+ x.start + "-" + x.end, args.bam, args.flank, repeats_fasta_folder + "/" + x._title + ".fa")
-            vis.alleleVisualiser(repeats_fasta_folder + "/" + x._title + ".fa", x.repeat_unit, args.flank, x._title, repeats_fasta_folder, x.chr, x.start, x.end, args.genome)
+            extract_repeats.fastaMaker(args.path_input_tsv, x.chr + ":"+ x.start + "-" + x.end, args.bam, args.flank, args.output + "/" + x._title + ".fa")
+            vis.alleleVisualiser(args.output + "/" + x._title + ".fa", x.repeat_unit, args.flank, x._title, args.output, x.chr, x.start, x.end, args.genome)
 
         print("Allele composition graphs completed.")
-        
+
+
 def main():
 
     loci_dict = ra.lociBedReader(args.loci_file)
     expansions = ra.resultBedReader(args.path_input_bed, loci_dict)
     sample_id = Path(args.path_input_bed).stem
-        
+
     vis.getHistData(args.path_input_tsv, expansions)
 
     for expansion_object in expansions:
+        if __name__ == '__main__':
+            expansion_object
         if args.altclust:
             ra.newGenotyping(expansion_object, args.cutoff, False)
 
@@ -142,7 +130,6 @@ def main():
         #Sorts expansion by chromosome
         expansions.sort(key=lambda x: x.chr)
 
-        
     outputWriter(expansions, sample_id, args)
 
 if __name__ == "__main__":