Is there a way to use custom matrix for nucleotide aligner in Biopython pairwise2 module? 
I want to decrease penalties for A->G, C->T substitutions.

    import Bio
    from Bio import pairwise2
    
    seq1='AGTCGATCATCGGA'
    seq2='ATTAGATCATCGGGGA'
    
    alignment = pairwise2.align.localms(seq1, seq2, 2,-1,-2,-1,one_alignment_only=True)
    print(format_alignment(*alignment[0]))

    AGTCGATCATCGGA--
    |.|.|||||||||
    ATTAGATCATCGGGGA
      Score=20
how about trying somethig like this

    import Bio
    from Bio import pairwise2
    from Bio.pairwise2 import format_alignment
    
    seq1 = 'AGTCGATCATCGGA'
    seq2 = 'ATTAGATCATCGGGGA'
    
    
    match_dic = {}
    match_dic[('A', 'A')] = 2
    match_dic[('A', 'C')] = -1
    match_dic[('A', 'T')] = -1
    match_dic[('A', 'G')] = 1
    match_dic[('C', 'A')] = -1
    match_dic[('C', 'C')] = 2
    match_dic[('C', 'T')] = 1
    match_dic[('C', 'G')] = -1
    match_dic[('G', 'A')] = -1
    match_dic[('G', 'C')] = -1
    match_dic[('G', 'T')] = -1
    match_dic[('G', 'G')] = 2
    match_dic[('T', 'A')] = -1
    match_dic[('T', 'C')] = -1
    match_dic[('T', 'T')] = 2
    match_dic[('T', 'G')] = -1
    
    alignment = pairwise2.align.localds(
        seq1, seq2, match_dic, -2, -1, one_alignment_only=True)
    print(alignment[0])
    print(format_alignment(*alignment[0]))

