How to add the misssing bases to a DNA sequence according to the hsp.start, and missing bases

Question

[bio90029]

Hi, I am working on a python script to curate the DNA sequence of a few genes. I initially perform a local blast, and now I am trying to add the missing bases. I have been trying and changing my script but I cannot get the right solution, and I keeping messing up and getting frustrated. I write below the part of the script that supposedly sort out the gene:

my_seq_1=None
if seq_length==ref_length:
    print 'Sequence length are equal'                               
    extracted_genes=(genes)
    output_handle.write(extracted_genes)
if seq_length!=ref_length:
    contig_files=(SeqIO.index(f + '/contigs.fa', 'fasta'))
    #to add missing bases
    if seq_start>seq_end:
        print  'The sequence is in strand -1 and need to be reversed first'
        if ref_start==1:
            #to calculate the missing bases                                     
            add_bases=int(ref_length) - int(len(contig_files[contig_name].seq[seq_end:seq_start]))
            end=int(seq_end)-int(add_bases)   #this is in reality the beginning of the seq
            my_seq_reverse=contig_files[contig_name].seq[end:seq_start]
            my_seq_1=my_seq_reverse.reverse_complement
            extracted_genes=(genes)
            output_handle.write(extracted_genes)
        if ref_start!=1:
            add_bases_1=int(ref_length) - int(len(contig_files[contig_name].seq[seq_end:seq_start]))
            #the end but the beginning of the reversed seq
            end=int(seq_end)-int(add_bases_1)
            start=int(seq_start)-int(ref_start)+add_bases_1                                                 
            my_seq_reverse_2=contig_files[contig_name].seq[end:start]                                                                               
            my_seq_1=my_seq_reverse_2.reverse_complement()
            extracted_genes=(genes)
            output_handle.write(extracted_genes)                                        
if seq_start<seq_end:
        print 'The sequence is in + strand'
        if ref_start==1: #this part of the script works well
            #only need to add the number of missing bases at the end of the seq
            add_end_2=int(ref_length) - int(len(contig_files[contig_name].seq[seq_start:seq_end]))
            end_2=int(seq_end)+int(add_end_2)
            # needs to start the seq one bases before due to the way python counts.
            my_seq_1=contig_files[contig_name].seq[seq_start-1:end_2-1]
            extracted_genes=(genes)
            output_handle.write(extracted_genes)
            #as the ref_start!=1. I need to add this bases at the start_seq and 
        if ref_start!=1:
            #the number of bases missing to have both seq and ref equal length
            add_end_3=int(ref_length) - int(len(contig_files[contig_name].seq[seq_start:seq_end]))
            # need to add the ref_start to the seq_start. So the seq stars few bases before
            start=int(seq_start)-int(ref_start)
            #need to remove the same number of bases at the end of seq but adding the missing bases.
            end=int(seq_end)-int(ref_start)+int(add_end_3)
            my_seq_1=contig_files[contig_name].seq[start:end]                                       
            extracted_genes= (genes)                                                                                    
            output_handle.write(extracted_genes)
I will be really greatful if someone can point me where are my mistakes as the script is not working as it is supposed to.

Thanks