RiE dZddlmZddlmZddlmZddlmZGddejZGdd ejZ y ) zBio.Align support for aligned FASTA files. Aligned FASTA files are FASTA files in which alignment gaps in a sequence are represented by dashes. Each sequence line in an aligned FASTA should have the same length. ) Alignment) interfaces)Seq) SeqRecordceZdZdZdZdZy)AlignmentWriterz8Alignment file writer for the aligned FASTA file format.FASTAct|ts tdg}t|j|D]z\}} |j }|j r,|jd|j d|j n|jd|j  |j||dj|dzS#t$r|jdYCwxYw)z;Return a string with the alignment in aligned FASTA format.zExpected an Alignment object>  ) isinstancer TypeErrorzip sequencesid descriptionappendAttributeErrorjoin)self alignmentlinessequencelinenames G/home/agent/.friday_env/lib/python3.12/site-packages/Bio/Align/fasta.pyformat_alignmentz AlignmentWriter.format_alignments)Y/:; ;!)"5"5yA NHd 4{{''LL1X[[M83G3G2H!IJLL1X[[M!23 LL  yy$&&" " S! "s CC"!C"N)__name__ __module__ __qualname____doc__fmtrrrrsB C'r%rceZdZdZdZdZy)AlignmentIteratoraAlignment iterator for aligned FASTA files. An aligned FASTA file contains one multiple alignment. Alignment gaps are represented by dashes in the sequence lines. Header lines start with '>' followed by the name of the sequence, and optionally a description. r cg}g}g}|D]}|jdr|ddjjdd}t|dk(r|\}}nd}t|dk(r|d}nd}|j ||j ||j d|dxx|j z cc<|s)|j jdk(r tdy|Dcgc]}|j}}tj|\} } g} t||| D]0\}}} t| } t| ||}| j |2t| | }|Scc}w) Nr rz Empty file.)rr) startswithrstripsplitlenrstrip_streamtell ValueErrorencoderparse_printed_alignmentrrr)rstreamnames descriptionsrrpartsrrseqs coordinatesrecordsseqrrecordrs r_read_next_alignmentz&AlignmentIterator._read_next_alignment6sn  *Ds#QR)//a8u:?(-%D+"$K5zQ$Qx! T"##K0 R b TZZ\)  * ||  "a' // +01411%==eDk&)%t&D # "D+s3xHxDkJF NN6 " #g{3 2s,E-N)rr r!r"r#r@r$r%rr'r',s C r%r'N) r" Bio.AlignrrBio.Seqr Bio.SeqRecordrrr'r$r%rrDs< #'j00'0* 44*r%