diff --git a/Functions_output.py b/Functions_output.py index 2ddf9ec232fd3e49aac898e18414bac0e7ecc10c..d40c8408f733fe1d4a8f49618e786d7c6e9068c4 100644 --- a/Functions_output.py +++ b/Functions_output.py @@ -245,12 +245,6 @@ def print_current_var(variation,feat_start,list_segfeat_azu,feat,i): line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tdeletion\t{variation.ref}\t-\t{len(variation.ref)}\t{pos_old}\t{pos_new}\n' write_line(line,output_variations,False) elif variation.type=='substitution': - - #Â detect inversions : look for segments common if we dont consider the orientation ? - # in nb : look for segment_i[1:] in azu. if not found, continue. if nb finished, no inv. - # if found ! : look for the next one. if not found, just print the inversion of 1 segment. - # what about inversions with indel/subs inside ?? - [pos_old,pos_new]=get_old_new_pos_substitution(feat_start,variation,list_segfeat_azu,feat) if len(variation.ref) == len(variation.alt): # if the substituion is between two segment of the same size, print it size_subs=len(variation.ref)