adapted the code to use the options for the output files. changed every...

adapted the code to use the options for the output files. changed every instance of 'clustal' to 'aln' in the code

Functions.py

@@ -38,9 +38,9 @@ def create_line_target_gff(first_seg,last_seg,feature_id,size_diff,list_seg):
     return output_line
 
 
-# functions to get the clustal alignment for the transfered genes
+# functions to get the alignment for the transfered genes
 
-# create clustal aln for a feature
+# create alignment for a feature
 def segment_aln(type,seg_seq,seg_a,seg_b):
 
     match type:
@@ -89,12 +89,12 @@ def segment_aln(type,seg_seq,seg_a,seg_b):
     return [line_a,line_b,line_c] # check the orientation of the segment later
 
 
-def parse_clustal_lines(line_a,line_b,line_c,feature_id):
+def parse_aln_lines(line_a,line_b,line_c,feature_id):
     if (len(line_a)!=len(line_b)) | (len(line_b)!=len(line_c)):
-        print("line length differ in clustal alignment")
+        print("line length differ in alignment")
     len_to_parse=len(line_a)
     len_parsed=0
-    clustal_line=""
+    aln_line=""
     nb_res_a=0
     nb_res_b=0
 
@@ -107,16 +107,16 @@ def parse_clustal_lines(line_a,line_b,line_c,feature_id):
         add_c=line_c[len_parsed:len_parsed+60]
         nb_res_a+=len(add_a)-add_a.count("-")
         nb_res_b+=len(add_b)-add_b.count("-")
-        clustal_line+=f'{headers[0]}{add_a}    {nb_res_a}\n'
-        clustal_line+=f'{headers[1]}{add_b}    {nb_res_b}\n'
-        clustal_line+=f'{headers[2]}{add_c}\n\n'
+        aln_line+=f'{headers[0]}{add_a}    {nb_res_a}\n'
+        aln_line+=f'{headers[1]}{add_b}    {nb_res_b}\n'
+        aln_line+=f'{headers[2]}{add_c}\n\n'
         len_parsed+=60
-    clustal_line+="\n"
+    aln_line+="\n"
     
-    return clustal_line
+    return aln_line
 
 
-def create_line_clustal(feature_path_source_genome,feature_path_target_genome,seg_seq,feature_id):
+def create_line_aln(feature_path_source_genome,feature_path_target_genome,seg_seq,feature_id):
     line_a=""
     line_b=""
     line_c=""
@@ -152,7 +152,7 @@ def create_line_clustal(feature_path_source_genome,feature_path_target_genome,se
         [add_a,add_b,add_c]=segment_aln("end_deletion",seg_seq,feature_path_source_genome[i:],"")
         line_a+=add_a;line_b+=add_b;line_c+=add_c
 
-    return parse_clustal_lines(line_a,line_b,line_c,feature_id)
+    return parse_aln_lines(line_a,line_b,line_c,feature_id)
 
 
 # functions to output the stats on the transfer

Functions_output.py

@@ -24,15 +24,15 @@ def generate_target_gff(first_seg,last_seg,feature_id,list_seg,max_diff):
 
 
 # writes the gff of target genome using the gff of the graph
-def transfer_on_target(segments_file, out_target_gff, out_var,out_clustal,target_genome,target_genome_paths,args):
+def transfer_on_target(segments_file, out_target_gff, out_var,out_aln,target_genome,target_genome_paths,args):
 
-    [target_gff,var,clustal,stats]=[True,True,True,False]
+    [target_gff,var,aln,stats]=[True,True,True,False]
     list_feature_to_transfer= Features.keys()
 
     print(f'generation of {target_genome} output')
     segments_list={}
 
-    if target_gff:
+    if args.annotation:
         print(f'    generation of {target_genome} gff')
         file_out=open(out_target_gff,'w')
         global output_target_gff
@@ -47,7 +47,7 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_clustal,target
             first_seg=get_first_seg(list_seg)[1:]
             last_seg=get_first_seg(reversed(list_seg))[1:]
 
-            if var: # append dict of segments for which we may need the sequence
+            if args.variation: # append dict of segments for which we may need the sequence
                 add_target_genome_path(feat,target_genome_paths)
                 for segment in list_seg:
                     segments_list[segment[1:]]=''
@@ -63,21 +63,21 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_clustal,target
                 diff_size_transfered_features[0]+=1
                 diff_size_transfered_features[1]+=transfer_stat
 
-    write_line("",output_target_gff,True)
-    file_out.close()
+        write_line("",output_target_gff,True)
+        file_out.close()
 
-    if var:
+    if args.variation:
         print(f'    generation of {target_genome} gene variation details')
         seg_seq=get_segments_sequence(segments_file,segments_list)
         file_out_var = open(out_var, 'w')
         global output_variations
         output_variations=[0,"",file_out_var]
 
-        if clustal:
-            file_clustal=open(out_clustal,'w')
-            global output_target_clustal
-            output_target_clustal=[0,"",file_clustal]
-            write_line("Sequence alignment generated from feature path comparison in pangenome graph. Made with GrAnnoT v1.\n\n",output_target_clustal,False)
+        if args.alignment:
+            file_aln=open(out_aln,'w')
+            global output_target_aln
+            output_target_aln=[0,"",file_aln]
+            write_line("Sequence alignment generated from feature path comparison in pangenome graph. Made with GrAnnoT v1.\n\n",output_target_aln,False)
 
         for feat in list_feature_to_transfer:
             # for each feature, get list of the segments where it is and the first and last segment of the feature on the new genome
@@ -87,10 +87,10 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_clustal,target
 
             print_variations(first_seg,last_seg,feat,seg_seq)
 
-    write_line("",output_variations,True)
-    write_line("",output_target_clustal,True)
-    file_out_var.close()
-    file_clustal.close()
+        write_line("",output_variations,True)
+        write_line("",output_target_aln,True)
+        file_out_var.close()
+        file_aln.close()
 
     if stats:
         # create objects for stats on how many segments are absent in target genome, their average length, etc
@@ -111,7 +111,7 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_clustal,target
         for feat in list_feature_to_transfer:
             stats_feature_missing_segment(feature_missing_segments,first_seg,last_seg,list_seg,feat)
 
-        if target_gff:
+        if args.annotation:
             print(len(Features)-(bad_size_features+absent_features),"out of",len(Features),"features are transfered.")
             print(bad_size_features,"out of",len(Features), "features are not transfered because they are too big or too small compared to the original genome.")
             print(absent_features,"out of",len(Features),"features are not transfered because they are absent in the new genome.")
@@ -132,8 +132,8 @@ def print_variations(first_seg,last_seg,feat,seg_seq):
         # loop to go through both paths with i and j
         [i,j,var_count]=[0,0,0]
 
-        line_clustal=create_line_clustal(feature_path_source_genome,feature_path_target_genome,seg_seq,feat)
-        write_line(line_clustal,output_target_clustal,False)
+        line_aln=create_line_aln(feature_path_source_genome,feature_path_target_genome,seg_seq,feat)
+        write_line(line_aln,output_target_aln,False)
 
         # detect and print variations ignoring the strands
         while (i<len(feature_path_source_genome)) & (j<len(feature_path_target_genome)):

main.py

@@ -22,8 +22,10 @@ out_graph_gaf=gfa.split("/")[-1].split(".")[0:-1][0]+".gaf"
 
 segments=args.segment_coordinates_path+"/segments.txt"
 
-graph_gff(out_graph_gff)
-graph_gaf(out_graph_gaf,segments)
+if args.graph_gff:
+    graph_gff(out_graph_gff)
+if args.graph_gaf:
+    graph_gaf(out_graph_gaf,segments)
 
 
 segment_coord_files=os.listdir(args.segment_coordinates_path)
@@ -59,6 +61,6 @@ for target_genome in args.target:
 
     out_target_gff=target_genome+"/"+target_genome+".gff"
     out_target_var=target_genome+"/"+target_genome+"_var.txt"
-    out_clustal=target_genome+"/"+target_genome+"_aln.txt"
+    out_aln=target_genome+"/"+target_genome+"_aln.txt"
 
-    transfer_on_target(segments,out_target_gff,out_target_var,out_clustal,target_genome,target_genome_paths,args)
+    transfer_on_target(segments,out_target_gff,out_target_var,out_aln,target_genome,target_genome_paths,args)