started changing transfer stats

GrAnnoT/setup_transfer.py

@@ -14,7 +14,7 @@ from tqdm import tqdm
 def transfer_on_target(segments_file,genome_dir,target_genome,target_genome_paths,list_feat_absent,seg_info,args,segments_on_target_genome):
 
     print(f'     Generating the {target_genome} output')
-    stats=False
+    stats=True
     list_feature_to_transfer= Features.keys()
     segments_list={} # list of segments usefull for the transfer. not all segments info will be loaded.
 
@@ -36,10 +36,12 @@ def transfer_on_target(segments_file,genome_dir,target_genome,target_genome_path
         with open(out_gff,'w') as file_out_gff:
             reason_features_not_transfered=[0,0] # absent_features, low_cov_id
             diff_size_transfered_features=[0,0] # [count,sum], to get the average
+            gene_count=0
 
             for feat in tqdm(list_feature_to_transfer,desc=f'        Generating {target_genome} gff',unit=" feature",disable=not args.verbose):
                 feature=Features[feat]
                 if feature.parent=="": # usually a gene
+                    gene_count+=1
                     for match in feature.segments_list_target: # compute cov and id for all matches.
                         if match.walk_name=='':
                             feature_target_path=[]
@@ -142,8 +144,16 @@ def transfer_on_target(segments_file,genome_dir,target_genome,target_genome_path
 
 
     if stats:
+
+        # print nb feat to transfer
+        absent_features=reason_features_not_transfered[0];low_cov_id=reason_features_not_transfered[1]
+        print(f'\n{len(Features)-(absent_features+low_cov_id)} out of {len(Features)} features are transferred on {target_genome}.')
+        print(f'{absent_features} out of {gene_count} main features are not transfered because they are absent in the haplotype {target_genome}.')
+        print(f'{low_cov_id} out of {gene_count} main features are not transfered because their coverage or sequence identity is below threshold.')
+        print(f'Average length difference of the transfered genes : {diff_size_transfered_features[1]/diff_size_transfered_features[0]}')
+
         # create objects for stats on how many segments are absent in target genome, their average length, etc
-        feature_missing_segments=[[],[],[],[],[],[],[]] # [feature_missing_first,feature_missing_middle,feature_missing_last,feature_missing_all,feature_missing_total,feature_total,feature_ok]
+        #feature_missing_segments=[[],[],[],[],[],[],[]] # [feature_missing_first,feature_missing_middle,feature_missing_last,feature_missing_all,feature_missing_total,feature_total,feature_ok]
         # the fist segment of the feature is missing - feature_missing_first
         # the last segment of the feature is missing - feature_missing_last
         # at least one middle segment of the feature is missing - feature_missing_middle
@@ -153,19 +163,13 @@ def transfer_on_target(segments_file,genome_dir,target_genome,target_genome_path
         # total number of features, with missing segments or not - feature_total
 
         # for each feature, get list of the segments where it is and the first and last segment of the feature on the new genome
-        list_seg=Features[feat].segments_list_source
-        match=Features[feat].segments_list_target[0]
-
-        for feat in list_feature_to_transfer:
-            stats_feature_missing_segment(feature_missing_segments,match.first_seg,match.last_seg,list_seg,feat,match.walk_name,segments_on_target_genome)
-
-        if args.annotation:
-            absent_features=reason_features_not_transfered[0];low_cov_id=reason_features_not_transfered[1]
-            print(len(Features)-(absent_features+low_cov_id),"out of",len(Features),"features are transfered.")
-            print(absent_features,"out of",len(Features),"features are not transfered because they are absent in the new genome.")
-            print(low_cov_id,"out of",len(Features),"features are not transfered because their coverage or sequence identity is below threshold.")
-            print("average length difference of the transfered genes : ",diff_size_transfered_features[1]/diff_size_transfered_features[0])
-        stats_features(feature_missing_segments)
+        #list_seg=Features[feat].segments_list_source
+        #match=Features[feat].segments_list_target[0]
+
+        #for feat in list_feature_to_transfer:
+        #    stats_feature_missing_segment(feature_missing_segments,match.first_seg,match.last_seg,list_seg,feat,match.walk_name,segments_on_target_genome)
+
+        #stats_features(feature_missing_segments)
 
     #clear segment info for next transfer
     segments_on_target_genome.clear() # empty dict for the next genome treated
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