o Rŀg@s\dZddlmZddlmZddlmZddlmZGdddejZGdd d ej Z d S) zBio.Align support for A2M files. A2M files are alignment files created by align2model or hmmscore in the SAM Sequence Alignment and Modeling Software System. ) Alignment) interfaces)Seq) SeqRecordc@s$eZdZdZdZddZejjZ dS)AlignmentWriterz.Alignment file writer for the A2M file format.A2Mc Cst|ts tdg}|jd}t|j|D]k\}}z|j}Wn ty*d}Ynwz|j}Wn ty;d}Ynw|rJ| d|d|n| d|d}t||D]"\} } | dkrh|| 7}qY| dkr{| dkru|d 7}qY|| 7}qY| |qd |d S) z:Return a string with the alignment in the A2M file format.zExpected an Alignment objectstate> DI-. ) isinstancer TypeErrorcolumn_annotationszip sequencesidAttributeError descriptionappendupperlowerjoin) self alignmentlinesrsequencelinenamerscmr&A/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/a2m.pyformat_alignments:         z AlignmentWriter.format_alignmentN) __name__ __module__ __qualname____doc__fmtr(rrwrite_single_alignmentwrite_alignmentsr&r&r&r'rs  rc@seZdZdZdZddZdS)AlignmentIteratoraAlignment iterator for files in the A2M file format. An A2M file contains one multiple alignment. Matches are represented by upper case letters and deletions by dashes in alignment columns containing matches or deletions only. Insertions are represented by lower case letters, with gaps aligned to the insertion shown as periods. Header lines start with '>' followed by the name of the sequence, and optionally a description. rc Cs g}g}g}|D]Q}|drO|dddd}z|d}Wn ty,d}Ynwz|d}Wn ty>d}Ynw|||||dq|d|7<q|si|jdkrgtddSd} |dD]!} | dksy| r~| d7} qo| d ks| r| d 7} qot d | |ddD]/}t || D]'\} } | dkr| dks| sJq| d kr| d ks| sJqt d | qt |D]\} }|d d|| <qt|\} }g}t ||| D]\}}}t|}t|||d }||qt||}i|_| |jd <|S)Nr rr z Empty file.rr rr z#Unexpected letter '%s' in alignment)rr) startswithrstripsplit IndexErrorrstrip_streamtell ValueErrorisupperislower Exceptionr enumeraterreplaceencoderparse_printed_alignmentrrr)rstreamnames descriptionsrr!partsr"rrr$r%iseqdata coordinatesrecordsseqrowr recordrr&r&r'_read_next_alignmentFsj                z&AlignmentIterator._read_next_alignmentN)r)r*r+r,r-rLr&r&r&r'r0:s r0N) r, Bio.AlignrrBio.Seqr Bio.SeqRecordrrr0r&r&r&r's    '