o Rŀg-"@sHdZddlmZddlmZddlmZddlmZGdddeZ dS) a\Bio.AlignIO support for "emboss" alignment output from EMBOSS tools. 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). This module contains a parser for the EMBOSS pairs/simple file format, for example from the alignret, water and needle tools. )MultipleSeqAlignment)AlignmentIterator)Seq) SeqRecordc@seZdZdZdZddZdS)EmbossIteratorzEmboss alignment iterator. For reading the (pairwise) alignments from EMBOSS tools in what they call the "pairs" and "simple" formats. Nc Csn|j}|jdur |}n|j}d|_|st|dkr+|}|s%t|dksd}d}g}i}|ddkr|dddd}|d}|dkrt|d}t |dks_Jt |D])} |}|dddd}| dt|dksJ| |dqct ||ksJ|dkrt|d}|d krt|dd d|d <|d krt|dd d|d <|d krt|dd d|d <|d krt |d|d <|}|ddks9|durt d|durt d|jdur|j|krt d||jfdgt |} g} d} |rmt |dkrD|dddd} |dddd}t | dkrBt |dkrB| \}}|\}}||kr}|dddkrrt|}t|}n$t|d}t|}n|dddksJt|t|d}t|}| dks| |krt d| |f||| ks||| dt |ksJt | | kr| |||kr|dddksJ|n'|| | t | | ddkrt dt | | dd| || | ||f| | |7<|| | t | | ddkr6t dt | | dd| || | | | ||f| d7} | |krAd} n n|dkrLnt d|d|}|dksf|dkrj||_n|s&| dkstJ|jdur|jt |krt dt ||jfg}t|| D]\}}t ||krt d| tt|||dqt||dS)z)Parse the next alignment from the handle.Nz(#=======================================r#:aligned_sequenceslengthidentity/ similaritygapsscorezNumber of sequences missing!zLength of sequences missing!z5Found %i records in this alignment, told to expect %i-z!Expected index %i in range [0,%i)zFFound %i chars so far for sequence %i (%s, %r), line says start %i: %szNFound %i chars so far for sequence %i (%s, %r, start=%i), file says end %i: %sz#Unrecognised EMBOSS pairwise line:  z(#---------------------------------------zeError parsing alignment - sequences of different length? You could be using an old version of EMBOSS.)id description) annotations)handle_headerreadline StopIterationrstripsplitlowerstripintlenrangeappendfloat ValueErrorrecords_per_alignmentreplacereprziprrr)selfrlinelength_of_seqsnumber_of_seqsids header_dictpartskeyiseqs seq_startsindexid_startseq_endrstartseqendrecordsr=H/var/www/html/myenv/lib/python3.10/site-packages/Bio/AlignIO/EmbossIO.py__next__s                ,  " " Y   zEmbossIterator.__next__)__name__ __module__ __qualname____doc__rr?r=r=r=r>rs rN) rC Bio.AlignrBio.AlignIO.InterfacesrBio.Seqr Bio.SeqRecordrrr=r=r=r>s