o RŀgB@sdZddlZddlmZddlmZddlmZddlm Z ddlm Z d Z d Z Gd d d e Z Gd dde ZGddde ZGdddeZGddde ZGdddeZdddZdS)aAlignIO support for "phylip" format from Joe Felsenstein's PHYLIP 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). Support for "relaxed phylip" format is also provided. Relaxed phylip differs from standard phylip format in the following ways: - No whitespace is allowed in the sequence ID. - No truncation is performed. Instead, sequence IDs are padded to the longest ID length, rather than 10 characters. A space separates the sequence identifier from the sequence. Relaxed phylip is supported by RAxML and PHYML. Note ==== In TREE_PUZZLE (Schmidt et al. 2003) and PHYML (Guindon and Gascuel 2003) a dot/period (".") in a sequence is interpreted as meaning the same character as in the first sequence. The PHYLIP documentation from 3.3 to 3.69 http://evolution.genetics.washington.edu/phylip/doc/sequence.html says: "a period was also previously allowed but it is no longer allowed, because it sometimes is used in different senses in other programs" Biopython 1.58 or later treats dots/periods in the sequence as invalid, both for reading and writing. Older versions did nothing special with a dot/period. N)MultipleSeqAlignment)Seq) SeqRecord)AlignmentIterator)SequentialAlignmentWriter z/PHYLIP format no longer allows dots in sequencec@eZdZdZefddZdS) PhylipWriterzPhylip alignment writer.cCs|j}t|dkr td|}|D] }|t|jkr tdq|dkr)tdg}g}|D]-} t|j|}||vrEtd||jf||t|j} d| vrWtt || q/| dt||fd} t ||D]H\}} | dkr| |d | |n| d |t d D]"} | d | d } | | | d } | d | | d |krnq| dqp| d7} | d |krd S| dqk)a&Use this to write (another) single alignment to an open file. This code will write interlaced alignments (when the sequences are longer than 50 characters). Note that record identifiers are strictly truncated to id_width, defaulting to the value required to comply with the PHYLIP standard. For more information on the file format, please see: http://evolution.genetics.washington.edu/phylip/doc/sequence.html http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles rMust have at least one sequence%Sequences must all be the same length Non-empty sequences are requiredz-PhylipIterator._is_header..FrrT)stripsplitrintr)r#linepartsnumber_of_seqsr&r0r0r1 _is_headers    zPhylipIterator._is_headercCs4|d|j}||jddd}||fS)zExtract the sequence ID from a Phylip line (PRIVATE). Returning a tuple containing: (sequence_id, sequence_residues) The first 10 characters in the line are are the sequence id, the remainder are sequence data. Nr)r%rBreplace)r#rEseq_idrr0r0r1 _split_idszPhylipIterator._split_idc Cs|j}|jdur |}n|j}d|_|st|}dd|D}t|dkr.tdzt|d}t|d}Wn tyHtddw| |sPJ|j durc|j |krctd||j fg}g}t |D]"}| }| |\} } || d | vrtt|| gqkd } d |kr|}|snd |ks|sn;| |r||_n2t |D])}|d d } d | vrtt||| |}|s|d|krtd q|snqddt||D} t| S))Parse the next alignment from the handle.NcSr;r0r0r<r0r0r1r?r@z+PhylipIterator.__next__..rA#First line should have two integersrr5Found %i records in this alignment, told to expect %irrITrzEnd of file mid-blockcss.|]\}}ttd||||dVqdS)rIrr* descriptionN)rrjoinr=r.sr0r0r1 s  z*PhylipIterator.__next__..)r_headerreadline StopIterationrBrCrrrDrHrecords_per_alignmentr"rstriprLrrrJr r r#rrErFrGr&idsr)r. sequence_idrTrecordsr0r0r1__next__s|               zPhylipIterator.__next__) r4r5r6r7r8r%rVrHrLr_r0r0r0r1r:s  r:cs eZdZdZfddZZS)RelaxedPhylipWriterzRelaxed Phylip format writer.cstdd|DD]tfddtjDrtdqt|dkr&d}n tdd|Dd}t||dS) z!Write a relaxed phylip alignment.css|]}|jVqdSN)rrBr=rTr0r0r1rUsz6RelaxedPhylipWriter.write_alignment..c3s|]}|vVqdSrar0)r=cr*r0r1rUsz&Whitespace not allowed in identifier: rrcss|] }t|jVqdSra)rrrBrbr0r0r1rUsN)anystring whitespacerrmaxsuperr2)r#r$r% __class__rdr1r2s z#RelaxedPhylipWriter.write_alignment)r4r5r6r7r2 __classcell__r0r0rjr1r`sr`c@seZdZdZddZdS)RelaxedPhylipIteratorzRelaxed Phylip format Iterator.cCs(|dd\}}|dd}||fS)zExtract the sequence ID from a Phylip line (PRIVATE). Returns a tuple containing: (sequence_id, sequence_residues) For relaxed format split at the first whitespace character. NrrrI)rCrBrJ)r#rErKr+r0r0r1rL&szRelaxedPhylipIterator._split_idN)r4r5r6r7rLr0r0r0r1rm#s rmc@r )SequentialPhylipWriterz Sequential Phylip format Writer.c Cs|j}t|dkr td|}|D] }|t|jkr tdq|dkr)tdg}|D]}t|j|}||vrBtd||jf||q-|dt||ft ||D]'\}}t |j}d|vritt ||d| ||||d qXdS) z'Write a Phylip alignment to the handle.rr r r rrrNr) rrrrrrrrrr rrr!) r#r$r%rr&r'r(r*r+r0r0r1r25s:      z&SequentialPhylipWriter.write_alignmentNr3r0r0r0r1rn2r9rnc@seZdZdZdZddZdS)SequentialPhylipIteratoraSequential Phylip format Iterator. The sequential format carries the same restrictions as the normal interleaved one, with the difference being that the sequences are listed sequentially, each sequence written in its entirety before the start of the next. According to the PHYLIP documentation for input file formatting, newlines and spaces may optionally be entered at any point in the sequences. Nc Cs|j}|jdur |}n|j}d|_|st|}dd|D}t|dkr.tdzt|d}t|d}Wn tyHtddw| |sPJ|j durc|j |krctd||j fg}g}t |D]X}| }| |\} } || t| |kr|}|sn(|d krqd | |d d g} t| |krtd t| |ft| |ksd | vrtt|| qk |}|sn | |r||_nqddt||D} t| S)rMNcSr;r0r0r<r0r0r1r?}r@z5SequentialPhylipIterator.__next__..rArNrrrOrIrz)Found a record of length %i, should be %irTcss(|]\}}tt||||dVqdS)rPN)rrrSr0r0r1rUs z4SequentialPhylipIterator.__next__..)rrVrWrXrBrCrrrDrHrYr"rZrLrrRrJrr rr[r0r0r1r_nsx                    z!SequentialPhylipIterator.__next__)r4r5r6r7rVr_r0r0r0r1roas rocCsL|}dD]}||d}qdD]}||d}q|dur$|d|}|S)zSanitise sequence identifier for output. Removes the banned characters "[]()" and replaces the characters ":;" with "|". The name is truncated to "width" characters if specified. z[](),rIz:;|N)rBrJ)r*widthcharr0r0r1rs rra)r7rf Bio.AlignrBio.Seqr Bio.SeqRecordr Interfacesrrr8rr r:r`rmrnrorr0r0r0r1s      ]~/X