{Ti7NdZddlmZddlmZddlmZddlmZGddeZ y ) aiBio.AlignIO support for GCG MSF format. The file format was produced by the GCG PileUp and and LocalPileUp tools, and later tools such as T-COFFEE and MUSCLE support it as an optional output format. The original GCG tool would write gaps at ends of each sequence which could be missing data as tildes (``~``), whereas internal gaps were periods (``.``) instead. This parser replaces both with minus signs (``-``) for consistency with the rest of ``Bio.AlignIO``. 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). )MultipleSeqAlignment)Seq) SeqRecord)AlignmentIteratorceZdZdZdZdZy) MsfIteratorzGCG MSF alignment iterator.NcJ|j}|j|j}n|j}d|_|stgd}|j j d|vr>t |j j dddj||rd|vr|j}|rd|vr|s t d|j dj }|jd }||d zd k7s|d d vs|ddk7rt d|z t||dz}|dkrt d||dzz||dz}|dvrt d|zg}g} g} g} |j}|r|j dk7r|j}|j jdrRd|vr?d|vr:d|vr5||jddzdj } | j d\} } | j d\}} | j d\}}| j } | jdr| dd } | |vrt d| d| vrtd| |j| | jt|j | jt|j | jt|j nt d ||r|j dk7r|s t d!|t| k7r:t| t!fd"| D}t d#||t#|fz|j}|s t d$|j r t d%|Dcgc]}g}}d}||kr!t%|D]\}} |j}|dk(rE|j s5|r3|j s#|j}|r|j s#|s t d&|j j }|dk(r|r|d| k7r t|d}||dzk7rt d'|dz|fzt#|dkDrSt#|d k7rd}n t|d}||d(z|kr|d(zn|k7r!t d)|dz|d(z|kr|d(zn||fz|j}|j j }|s>| ||kr%t#d*j||| |k(rt d+| d,||d| k(r.t#|dkDsJ|||j'|ddt d+| d,||d(z }|j}|j rt d-|||kr! |j}|snK|j sn9|j j d|vr||_nt d/|^|Dcgc]3}d*j|j)d0d1j)d2d15}}d3}t%t+| |D]?\}\}}t#||kst#||k(s'd.}|d1|t#|z zz||<A|rddl}dd4lm}|j3d5|d6t+||| D}t5|}|j7|k7rt d7||j7fz|S#t $rd}Y4wxYwcc}w#t $rd}YwxYw#t $rd}YwxYwcc}w)8z)Parse the next alignment from the handle.N)z!!NA_MULTIPLE_ALIGNMENTz!!AA_MULTIPLE_ALIGNMENTPileUprz is not a known GCG MSF header: z, z MSF: z6Reached end of file without MSF/Type/Check header line zMSF:zType:)zCheck:z CompCheck:z..zsGCG MSF header line should be ' MSF: Type: Check: ..', not: %rrzCGCG MSF header line should have MDF: for column count, not %r)PNz]GCG MSF header line should have 'Type: P' (protein) or 'Type: N' (nucleotide), not 'Type: %s'z//zName: z Len: z Check: z Weight: z oozDuplicated ID of  z Space in ID zMalformed GCG MSF name line: z4End of file while looking for end of header // line.c3.K|] }|k(s dyw)rN).0_ max_lengths D/home/agent/.local/lib/python3.12/site-packages/Bio/AlignIO/MsfIO.py z'MsfIterator.__next__..sB!!z/ABs zLGCG MSF header said alignment length %i, but %s of %i sequences said Len: %sz.End of file after // line, expected sequences.z4After // line, expected blank line before sequences.z*End of file where expecting sequence data.z5Expected GCG MSF coordinate line starting %i, got: %r2z2Expected GCG MSF coordinate line %i to %i, got: %rzExpected sequence for z, got: zExpected blank line, got: Tz)Unexpected line after GCG MSF alignment: ~-.F)BiopythonParserWarningzGOne of more alignment sequences were truncated and have been gap paddedc 3ZK|]#\}}}tt||||d|i%yw)weight)idname description annotationsN)rr)risws rrz'MsfIterator.__next__..@s7 Aq c!fRS} U U s)+z5GCG MSF headers said alignment length %i, but have %i)handle_headerreadline StopIterationstripsplit ValueErrorjoinindexint startswithendswithNotImplementedErrorappendfloatmaxsumlen enumerateextendreplacezipwarningsBior!warnrget_alignment_length)selfr+line known_headerspartsoffset aln_lengthseq_typeidslengthschecksweightsrestr%lengthcheckr# max_countrseqscompleted_lengthidxwordsr(r)paddedrAr!recordsalignrs @r__next__zMsfIterator.__next__#s( << ??$D<U #$ !$ : %<>FG & tzz|t+??$Dzz|&&x0t# d(:{d?R 8 4q 8 :;AACD!%H!5JD$#'::j#9LFD$(JJ{$;ME6::/4/>I$$U12Y/$'=dXWTH%UVVKE WP  " ??$Dzz| #=dX!FGG[+`??$DZZ\##%a(M9#  #LTH!UVV IMM1 ""3,44S#>MM )#gt*< = < C&!1v "s1v'7zCF': ;;S  <   2 MMY&    dG4  %W-  % % ': 5Gu99;<=  [ J X!(&$.'$&'@NsB.]% ]7]<^"8^ % ]43]4< ^  ^  ^^)__name__ __module__ __qualname____doc__r,r[rrr r s%Gjr`r N) r_ Bio.AlignrBio.Seqr Bio.SeqRecordr Interfacesrr rr`rres' +#)o#or`