added a few progress bars

GrAnnoT/Functions_output.py

 from .Graph_gff import Segments, Features
 from .Functions import *
+from tqdm import tqdm
 
 
 # outputs the gff line of the target genome for a feature occurence (a feature can be transfered at several positions)
@@ -106,7 +107,7 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_aln,target_gen
             reason_features_not_transfered=[0,0,0] # bad_size, absent_features, low_cov_id
             diff_size_transfered_features=[0,0] # [count,sum], to get the average
 
-            for feat in list_feature_to_transfer:
+            for feat in tqdm(list_feature_to_transfer):
                 feature=Features[feat]
                 if feature.parent=="": # usually a gene
                     for match in feature.segments_list_target:
@@ -149,7 +150,7 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_aln,target_gen
         seg_seq=get_segments_sequence(segments_file,segments_list)
         with open(out_var, 'w') as file_out_var:
 
-            for feat in list_feature_to_transfer:
+            for feat in tqdm(list_feature_to_transfer):
                 feature=Features[feat]
                 if feature.parent=="": # usually a gene
                     for match in feature.segments_list_target: # for all occurences of the gene
@@ -163,7 +164,7 @@ def transfer_on_target(segments_file, out_target_gff, out_var,out_aln,target_gen
             line="Sequence alignment generated from feature path comparison in pangenome graph. Made with GrAnnoT v1.\n\n"
             file_out_aln.write(line)
 
-            for feat in list_feature_to_transfer:  
+            for feat in tqdm(list_feature_to_transfer):  
                 feature=Features[feat]
                 if feature.parent=="": # usually a gene
                     for match in feature.segments_list_target: # for all occurences of the gene