o RŀgX@sdZddlmZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z  dd eed eed eefd dZGddde ZedkrXddlmZeddd Sd S)aiBio.AlignIO support for the "nexus" file format. You are expected to use this module via the Bio.AlignIO functions (or the Bio.SeqIO functions if you want to work directly with the gapped sequences). See also the Bio.Nexus module (which this code calls internally), as this offers more than just accessing the alignment or its sequences as SeqRecord objects. )IO)Iterator)Optional)MultipleSeqAlignment)AlignmentWriter)Nexus) SeqRecordNhandle seq_countreturnc#st|js dStjtjksJ|r+|tjkr+tdtj|fjdvr5ddinjdkr?ddin jdkrIddindfd d tjjD}t|VdS) aUReturn SeqRecord objects from a Nexus file. Thus uses the Bio.Nexus module to do the hard work. You are expected to call this function via Bio.SeqIO or Bio.AlignIO (and not use it directly). NOTE - We only expect ONE alignment matrix per Nexus file, meaning this iterator will only yield one MultipleSeqAlignment. Nz$Found %i sequences, but seq_count=%i)dna nucleotide molecule_typeDNArnaRNAproteinc3s,|]\}}tj|||ddVqdS))idname description annotationsN)rmatrix).0old_namenew_namernG/var/www/html/myenv/lib/python3.10/site-packages/Bio/AlignIO/NexusIO.py Es z NexusIterator..) rrlenunaltered_taxlabels taxlabels ValueErrordatatypezipr)r r recordsrrr NexusIterators,           r(c@s*eZdZdZddZd ddZddZdS) NexusWriterzNexus alignment writer. Note that Nexus files are only expected to hold ONE alignment matrix. You are expected to call this class via the Bio.AlignIO.write() or Bio.SeqIO.write() functions. cCs\t|}zt|}Wn tyYdSwzt|tdty&Ynw||dS)zUse this to write an entire file containing the given alignments. Arguments: - alignments - A list or iterator returning MultipleSeqAlignment objects. This should hold ONE and only one alignment. rz0We can only write one Alignment to a Nexus file.)iternext StopIterationr$write_alignment)self alignments align_iter alignmentrrr write_file]s    zNexusWriter.write_fileNcCst|dkr td|}|dkrtd||}d|}t|}|D].}|dkr9d|jvr9t|jd|dkrJd |jvrJt|jd ||jt|jq&|d ur]|d k}|j |j |d d S)aWrite an alignment to file. Creates an empty Nexus object, adds the sequences and then gets Nexus to prepare the output. Default interleave behaviour: Interleave if columns > 1000 --> Override with interleave=[True/False] rzMust have at least one sequencez Non-empty sequences are requiredzF#NEXUS begin data; dimensions ntax=0 nchar=0; format datatype=%s; end;r Uz contains U, but DNA alignmentrTz contains T, but RNA alignmentNi) interleave) r!r$get_alignment_length_classify_mol_type_for_nexusrseqr add_sequencestrwrite_nexus_datar )r/r2r6columnsr%minimal_recordrrecordrrrr.ws(   zNexusWriter.write_alignmentcCsXdd|D}tdd|DrdStdd|DrdStdd|Dr(d Std ) zReturn 'protein', 'dna', or 'rna' based on records' molecule type (PRIVATE). All the records must have a molecule_type annotation, and they must agree. Raises an exception if this is not possible. cSsh|] }|jddqS)rN)rgetr_rrr sz;NexusWriter._classify_mol_type_for_nexus..cs|] }|o d|vVqdS)rNrrArrrr z;NexusWriter._classify_mol_type_for_nexus..r csrD)rNrrArrrr rErcsrD)rNrrArrrr rErz$Need the molecule type to be defined)allr$)r/r2valuesrrrr8sz(NexusWriter._classify_mol_type_for_nexusN)__name__ __module__ __qualname____doc__r3r.r8rrrrr)Ss   r)__main__) run_doctest)verboserH)rLtypingrcollections.abcrr Bio.AlignrBio.AlignIO.Interfacesr Bio.Nexusr Bio.SeqRecordrr;intr(r)rI Bio._utilsrNrrrrs*       4W