add afunction format

frangiPANe/snakemake_scripts/vecscreen.py

 from Bio import SeqIO
 import os
 import sys
+
+def format_60(txt):
+    output = ''
+    cpt = 0
+    for c in txt:
+        if cpt < 60:
+            output += c
+            cpt += 1
+        else:
+            output += '\n' + c
+            cpt = 1
+    return (output)
+
 nb_seq, nb_seq_no_hits, nb_seq_suspicious = 0, 0, 0
 
 if len(sys.argv) >= 3:
@@ -16,7 +29,7 @@ with open(os.path.join(output_fasta), "w") as o:
 
             with open(tmp_file, "w") as tmp:
                 tmp.write('>' + str(seq.description) + '\n')
-                tmp.write(gs.format_60(str(seq.seq)) + '\n')
+                tmp.write(format_60(str(seq.seq)) + '\n')
 
             cmd = f'vecscreen -db {input_univec} -query {tmp_file} -outfmt 1 -text_output'
             print(f"\t\t\ {seq.description} : vecscreen cmd : {cmd}")
@@ -30,7 +43,7 @@ with open(os.path.join(output_fasta), "w") as o:
 
             if 'No hits found' in process.stdout:
                 o.write('>' + str(seq.description) + '\n')
-                o.write(gs.format_60(str(seq.seq)) + '\n')
+                o.write(format_60(str(seq.seq)) + '\n')
                 nb_seq += 1
                 nb_seq_no_hits += 1
             else:
@@ -54,7 +67,7 @@ with open(os.path.join(output_fasta), "w") as o:
                         header_fields = str(seq.description).split()
                         o.write('>' + header_fields[0] + " " + str(new_length) + " " + " ".join(
                             header_fields[2:]) + '\n')
-                        o.write(gs.format_60(str(seq.seq[min_seq:max_seq])) + '\n')
+                        o.write(format_60(str(seq.seq[min_seq:max_seq])) + '\n')
                         nb_seq += 1
                 elif max_bounds == max_seq:
                     max_seq = min_bounds
@@ -63,7 +76,7 @@ with open(os.path.join(output_fasta), "w") as o:
                         header_fields = str(seq.description).split()
                         o.write('>' + header_fields[0] + " " + str(new_length) + " " + " ".join(
                             header_fields[2:]) + '\n')
-                        o.write(gs.format_60(str(seq.seq[min_seq:max_seq])) + '\n')
+                        o.write(format_60(str(seq.seq[min_seq:max_seq])) + '\n')
                         nb_seq += 1
                 else:
                     print("Warning (seq : " + str(