o Rŀg3@sdZddlZddlmZddlmZddlmZddlm Z ddlm Z e d Z e d Z d Zd d ZGddde ZGddde ZdS)aU Bio.AlignIO support for "xmfa" output from Mauve/ProgressiveMauve. 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). For example, consider a progressiveMauve alignment file containing the following:: #FormatVersion Mauve1 #Sequence1File a.fa #Sequence1Entry 1 #Sequence1Format FastA #Sequence2File b.fa #Sequence2Entry 2 #Sequence2Format FastA #Sequence3File c.fa #Sequence3Entry 3 #Sequence3Format FastA #BackboneFile three.xmfa.bbcols > 1:0-0 + a.fa -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- > 2:5417-5968 + b.fa TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACGTGAGAGGAGCGCCCTAAGCTTTGGGAAATTCAAGC- -------------------------------------------------------------------------------- CTGGAACGTACTTGCTGGTTTCGCTACTATTTCAAACAAGTTAGAGGCCGTTACCTCGGGCGAACGTATAAACCATTCTG > 3:9476-10076 - c.fa TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-GGGAGGAGATCGCCCCAAACGTATGGTGAGTCGGGCG TTTCCTATAGCTATAGGACCAATCCACTTACCATACGCCCGGCGTCGCCCAGTCCGGTTCGGTACCCTCCATGACCCACG ---------------------------------------------------------AAATGAGGGCCCAGGGTATGCTT = > 2:5969-6015 + b.fa ----------------------- GGGCGAACGTATAAACCATTCTG > 3:9429-9476 - c.fa TTCGGTACCCTCCATGACCCACG AAATGAGGGCCCAGGGTATGCTT This is a multiple sequence alignment with multiple aligned sections, so you would probably load this using the Bio.AlignIO.parse() function: >>> from Bio import AlignIO >>> align = AlignIO.parse("Mauve/simple_short.xmfa", "mauve") >>> alignments = list(align) >>> for aln in alignments: ... print(aln) ... Alignment with 3 rows and 240 columns --------------------------------------------...--- a.fa TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACG...CTG b.fa/5416-5968 TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-G...CTT c.fa/9475-10076 Alignment with 2 rows and 46 columns -----------------------GGGCGAACGTATAAACCATTCTG b.fa/5968-6015 TTCGGTACCCTCCATGACCCACGAAATGAGGGCCCAGGGTATGCTT c.fa/9428-9476 Additional information is extracted from the XMFA file and available through the annotation attribute of each record:: >>> for record in alignments[0]: ... print(record.id, len(record)) ... print(" start: %d, end: %d, strand: %d" %( ... record.annotations['start'], record.annotations['end'], ... record.annotations['strand'])) ... a.fa 240 start: 0, end: 0, strand: 1 b.fa/5416-5968 240 start: 5416, end: 5968, strand: 1 c.fa/9475-10076 240 start: 9475, end: 10076, strand: -1 N)MultipleSeqAlignment)Seq) SeqRecord)AlignmentIterator)SequentialAlignmentWriterzG> (?P\d+):(?P\d+)-(?P\d+) (?P[+-]) (?P.*)z]> (?P\d+):(?P\d+)-(?P\d+) (?P[+-]) (?P[^#]*) # (?P.*)z<> {seq_name}:{start}-{end} {strand} {filename} # {ugly_hack}cCs8|d\}}}tt|d\}}|d8}||||fS)zDReturn (name, start, end) string tuple from an identifier (PRIVATE).:-r)splitmapint) identifieridlocstrandstartendrG/var/www/html/myenv/lib/python3.10/site-packages/Bio/AlignIO/MauveIO.py_identifier_splitbs rcs2eZdZdZfddZddZd ddZZS) MauveWriterzMauve/XMFA alignment writer.cs"tj|i|d|_d|_dS)zInitialize the class.FN)super__init__ _wrote_header _wrote_first)selfargskwargs __class__rrrms zMauveWriter.__init__cCst|}||_|dkrtd|jdkrtd|js=d|_|jdtd|dD]}|jd|d|d q-t|D] \}}|j ||d qA|jd d S) zUse this to write (another) single alignment to an open file. Note that sequences and their annotation are recorded together (rather than having a block of annotation followed by a block of aligned sequences). rzMust have at least one sequencez Non-empty sequences are requiredTz#FormatVersion Mauve1 rz #SequencezEntry  ) record_idxz= N) lenget_alignment_length_length_of_sequences ValueErrorrhandlewriterange enumerate _write_record)r alignmentcountiidxrecordrrrwrite_alignmentss   zMauveWriter.write_alignmentrc CsB|jt|jkr td|j}z tt|j}Wnty't|d}Ynwd|jvrxd|jvrxd|jdd|jd}d|jddd|jd}|t| d|krd|dt| }|t| d|krx|dt| }d|jvrd|jvrd|jvrtj ||jdd|jd|jddkrd nd|jd |j d }d }ntj |d d d |jd |j d }d}d|vsd|vr|s|j sd|_ tj |d d d |jd |j d }| dd dd}|j |ddSdS| dd dd}|j |dtd t|jdD]}|j |j||ddq dS)z/Write a single SeqRecord to the file (PRIVATE).z%Sequences must all be the same lengthrrr/r Nr+z.fa)seq_namerrrfilename ugly_hackFrTz:0-0 z:1-0 r   z P)r$r"seqr%namestrr annotations ID_LINE_FMTformatrrreplacer&r'r() rr/r!r3suffix0suffix1id_linelacking_annotationsr-rrrr*sn      $zMauveWriter._write_record)r)__name__ __module__ __qualname____doc__rr0r* __classcell__rrrrrjs  !rc@s*eZdZUdZgZeeed<ddZdS) MauveIteratorzMauve xmfa alignment iterator._idsc Cs2|j}|}|s t|r!|dr!|}|r!|dsi}i}d}d} |s-n|}|dr7n|drt|}|sOt|}|sOtd|| d}i} d D].} z#| | } | d krpt | } | d krp| d 8} | d krxt | } | | | <WqXt yYqXw| ||<||j vr|j |||d|}n|rJ|durtd|||7<|}q*t|t|j ksJ|j |_||_|j r|rtttt|} g} |j D]}||vst||d kst||d krd| }n||}| t|kr td||vrq||d d ks#||d d krNdjdi||}d||vr;||d}n||d}||d krM||7}nd||vr\||d}n||d}tt|||d}||d |jd <||d |jd <||ddkrd nd|jd<| |qt| St)z)Parse the next alignment from the handle.#FNT=>zMalformed header line: %sr)rrrrr:realnamerrrrz#Saw sequence before definition liner z8Sequences have different lengths, or repeated identifierz/{start}-{end}rNr:)rr:rr2r)r&readline StopIterationstrip startswithXMFA_HEADER_REGEX_BIOPYTHONmatchXMFA_HEADER_REGEXr%groupr IndexErrorrJappend setdefaultr"ids sequencesmaxr listvaluesr>r,rrr<r)rr&lineseqs seq_regionspassed_end_alignment latest_idm parsed_id parsed_datakeyvaluealignment_lengthrecordsrr9suffix corrected_idr/rrr__next__s            0 (  $   zMauveIterator.__next__N) rDrErFrGrJr_r;__annotations__rorrrrrIs  rI)rGre Bio.AlignrBio.Seqr Bio.SeqRecordr InterfacesrrcompilerWrUr=rrrIrrrrs"I     u