removed old code for transfer stat

GrAnnoT/compute_transfer_stat.py

-
-from .intersect import Features
-# functions to output the stats on the transfer
-
-# stats about missing segments and feature type, not used, will change.
-def stats_feature_missing_segment(feature_missing_segments,first_seg,last_seg,list_seg,feature_id,walk,segments_on_target_genome):
-# [feature_missing_first,feature_missing_middle,feature_missing_last,feature_missing_all,feature_missing_total,feature_total,feature_ok]
-    feature_missing_segments[5].append(feature_id)
-
-    if first_seg=='' : # no segment of the feature is in the genome, the feature is missing entirely
-        feature_missing_segments[3].append(feature_id)
-    elif first_seg != list_seg[0]: # the first segment is missing 
-        feature_missing_segments[0].append(feature_id)
-    elif last_seg!=list_seg[-1]: # the last segment is missing
-        feature_missing_segments[2].append(feature_id)
-
-    # go through all the segments, check if some are missing in the middle of the feature
-    elif (len(list_seg)!=1) and (feature_id not in feature_missing_segments[3]): # to access the second to last element
-        for segment in list_seg[1-(len(list_seg)-2)]:
-            if (segment not in segments_on_target_genome) or (not segments_on_target_genome[segment].find_filename(walk)):
-                feature_missing_segments[1].append(feature_id)
-                break
-
-    # go through the segments, to see if one is missing anywhere on the feature
-    for segment in list_seg:
-        if (segment not in segments_on_target_genome) or (not segments_on_target_genome[segment].find_filename(walk)):
-            if feature_id not in feature_missing_segments[4]:
-                feature_missing_segments[4].append(feature_id)
-                break
-
-    # if the feature doesnt have a missing segment, it is complete.         ADD THE PATH CHECK FOR INSERTIONS !!
-    if feature_id not in feature_missing_segments[4]:
-        feature_missing_segments[6].append(feature_id)
-
-def get_annot_features(list_features):
-    list_annot_features=[]
-    for feature in list_features:
-        list_annot_features.append(Features[feature].note)
-    return list_annot_features
-
-def count_hypput_total(list_annot_first):
-    total=len(list_annot_first)
-    count_hypput=0
-    for annot in list_annot_first:
-        if ("hypothetical" in annot) or ("putative" in annot):
-            count_hypput+=1
-    return [count_hypput,total]
-
-# print stats on the transfer : number of feature that have segments in different positions missing. 
-def stats_features(feature_missing_segments):
-# [feature_missing_first,feature_missing_middle,feature_missing_last,feature_missing_all,feature_missing_total,feature_total,feature_ok]
-    list_annot_first=get_annot_features(feature_missing_segments[0])
-    [hyp_put,total]=count_hypput_total(list_annot_first)
-    print("\nthe first segment is missing for", total,"features, including",round(100*(hyp_put)/total,2),"% hypothetical or putative.")
-
-    list_annot_middle=get_annot_features(feature_missing_segments[1])
-    [hyp_put,total]=count_hypput_total(list_annot_middle)
-    print("a middle segment is missing for", total,"features, including",round(100*(hyp_put)/total,2),"% hypothetical or putative.")
-
-    list_annot_last=get_annot_features(feature_missing_segments[2])
-    [hyp_put,total]=count_hypput_total(list_annot_last)
-    print("the last segment is missing for", total,"features, including",round(100*(hyp_put)/total,2),"% hypothetical or putative.")
-
-    list_annot_all=get_annot_features(feature_missing_segments[3])
-    [hyp_put,total]=count_hypput_total(list_annot_all)
-    print(total,"features are entirely missing, including",round(100*(hyp_put)/total,2),"% hypothetical or putative.")
-
-    list_annot_total=get_annot_features(feature_missing_segments[4])
-    [hyp_put,total]=count_hypput_total(list_annot_total)
-    print("there is at least one segment missing for", total,"features, including",round(100*(hyp_put)/total,2),"% hypothetical or putative.")
-
-    list_annot_ok=get_annot_features(feature_missing_segments[6])
-    [hyp_put,total]=count_hypput_total(list_annot_ok)
-    print(total ,"features are entirely present in the new genome, including",round(100*(hyp_put)/total,2),"% hypothetical or putative.")
-
-    list_annot_features=get_annot_features(feature_missing_segments[5])
-    [hyp_put,total]=count_hypput_total(list_annot_features)
-    print("there is", total,"features in total, including",round(100*(hyp_put)/total,2),"% hypothetical or putative.")
-
-