Bio.Codonalign包

子模块

• Bio.Codonalign. Codonalign模块
  • CodonAlignment
    • CodonAlignment.__init__()
    • CodonAlignment.__str__()
    • CodonAlignment.__getitem__()
    • CodonAlignment.__add__()
    • CodonAlignment.get_aln_length()
    • CodonAlignment.toMultipleSeqAlignment()
    • CodonAlignment.get_dn_ds_matrix()
    • CodonAlignment.get_dn_ds_tree()
    • CodonAlignment.from_msa()
    • CodonAlignment.__annotations__
    • CodonAlignment.__firstlineno__
    • CodonAlignment.__static_attributes__
  • mktest()
• Bio. Codonign.Codonseq模块
  • CodonSeq
    • CodonSeq.__init__()
    • CodonSeq.get_codon()
    • CodonSeq.get_codon_num()
    • CodonSeq.translate()
    • CodonSeq.toSeq()
    • CodonSeq.get_full_rf_table()
    • CodonSeq.full_translate()
    • CodonSeq.ungap()
    • CodonSeq.from_seq()
    • CodonSeq.__abstractmethods__
    • CodonSeq.__annotations__
    • CodonSeq.__firstlineno__
    • CodonSeq.__static_attributes__
  • cal_dn_ds()

模块内容

处理密码子比对的代码。

Bio.codonalign.build(pro_align, nucl_seqs, corr_dict=None, gap_char='-', unknown='X', codon_table=None, complete_protein=False, anchor_len=10, max_score=10)

根据蛋白质比对和相应的核酸构建密码子比对。

论点：

• pro_ign-蛋白质MultipleSeqign对象

• nucl_seqs -由SeqIO.parse或SeqIO.index或SeqRecord的集合返回的对象。

• corr_dict -将蛋白质id映射到核苷酸id的dict

• complete_protein -序列是否以起始密码子开始

返回CodonAlliance对象。

下面的例子回答了Biostar问题：https://www.biostars.org/p/89741/

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> from Bio.Align import MultipleSeqAlignment
>>> from Bio.codonalign import build
>>> seq1 = SeqRecord(Seq('ATGTCTCGT'), id='pro1')
>>> seq2 = SeqRecord(Seq('ATGCGT'), id='pro2')
>>> pro1 = SeqRecord(Seq('MSR'), id='pro1')
>>> pro2 = SeqRecord(Seq('M-R'), id='pro2')
>>> aln = MultipleSeqAlignment([pro1, pro2])
>>> codon_aln = build(aln, [seq1, seq2])
>>> print(codon_aln)
CodonAlignment with 2 rows and 9 columns (3 codons)
ATGTCTCGT pro1
ATG---CGT pro2