Merge branch 'master' of github.com:INRA-LPGP/radseq_analyses_pipeline

radseq_analysis/file_handler/positions.py

@@ -6,11 +6,12 @@ def load_positions_list(positions_file_path, global_parameters):
 
     with open(positions_file_path) as positions_file:
         for line in positions_file:
-            try:
-                fields = line[:-1].split('\t')
-                positions.append(tuple([int(fields[0]), int(fields[1])]))
-            except IndexError:
-                print('Error: cannot read positions file')
-                exit(1)
+            if line[:-1]:
+                try:
+                    fields = line[:-1].split('\t')
+                    positions.append(tuple([int(fields[0]), int(fields[1])]))
+                except IndexError:
+                    print('Error: cannot read positions file')
+                    exit(1)
 
     global_parameters.positions_list = positions

radseq_analysis/modules/blast.py

@@ -13,7 +13,11 @@ TODO: better system calls (check for errors)
 def create_temp_seq_file(sequences, species):
 
     temp_sequences_name = species + '_sequences.temp'
-
+    read_lengths = {len(data.sequence) for locus, data in sequences.items()}
+    if len(read_lengths) == 1:
+        read_length = list(read_lengths)[0]
+    else:
+        exit('Error: input sequences have variable lengths')
     with open(temp_sequences_name, 'w') as o:
         for locus_id, locus in sequences.items():
             o.write('>' +
@@ -21,6 +25,7 @@ def create_temp_seq_file(sequences, species):
                     str(locus.n_males) + '_' +
                     str(locus.n_females) + '\n')
             o.write(locus.sequence + '\n')
+    return read_length
 
 
 def create_temp_catalog_file(catalog_data, species):
@@ -75,24 +80,23 @@ def cleanup_temp_files(species):
     os.remove(temp_db_logs_name)
 
 
-def filter_blast_output(species):
+def filter_blast_output(species, read_length, n_mismatches=4):
 
     stacks = defaultdict(lambda: dict())
     temp_blast_results_name = species + '_blast_results.temp'
     results = open(temp_blast_results_name)
     for line in results:
         fields = line[:-1].split('\t')
-        if fields[2] == '94' and int(fields[3]) >= 90:
+        if fields[2] == str(read_length) and int(fields[3]) >= read_length - n_mismatches:
             stacks[fields[0]][fields[1]] = [fields[3], fields[4], fields[5]]
-
     return stacks
 
 
 def get_matching_sequences(sequences, catalog_data, species):
-    create_temp_seq_file(sequences, species)
+    read_length = create_temp_seq_file(sequences, species)
     create_temp_catalog_file(catalog_data, species)
     create_blast_db(species)
     run_blast(species)
-    stacks = filter_blast_output(species)
+    stacks = filter_blast_output(species, read_length=read_length, n_mismatches=4)
     cleanup_temp_files(species)
     return stacks

radseq_analysis/parameters/parser.py

@@ -131,7 +131,7 @@ Options:  -i\t--input-folder\tPath to a folder containing the output of denovo_m
     def rescue(self):
         parser = argparse.ArgumentParser(
             description='Regroup stacks into alleles after analysis',
-            usage='''python3 radseq_analysis.py rescue -i input_folder -s sequences_file [-c coverage_file -o output_file]
+            usage='''python3 radseq_analysis.py rescue -i input_folder -m popmap -s sequences_file [-c coverage_file -o output_file]
 
 Options:  -i\t--input-folder\tPath to a folder containing the output of denovo_map
 \t  -s\t--sequences\tPath to sequences file (result of haplotypes analysis)
@@ -161,11 +161,7 @@ Options:  -i\t--input-folder\tPath to a folder containing the output of denovo_m
             parser.print_usage()
             print()
             exit(1)
-        if not args.popmap or not os.path.isfile(args.popmap):
-            print('\nError: no valid popmap file specified\n')
-            parser.print_usage()
-            print()
-            exit(1)
+
         analysis(input_dir=args.input_folder,
                  sequences_file_path=args.sequences,
                  popmap_file_path=args.popmap,