:>"^K4@sdZddlmZddlZddlmZddlmZddlm Z ddl m Z dd l m Z ej d Zej d Zd Zd dZGddde ZGddde ZdS)a 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) ... SingleLetterAlphabet() alignment with 3 rows and 240 columns --------------------------------------------...--- a.fa TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACG...CTG b.fa/5416-5968 TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-G...CTT c.fa/9475-10076 SingleLetterAlphabet() 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 )print_functionN)Seq) SeqRecord)MultipleSeqAlignment)AlignmentIterator)SequentialAlignmentWriterzG> (?P\d+):(?P\d+)-(?P\d+) (?P[+-]) (?P.*)z]> (?P\d+):(?P\d+)-(?P\d+) (?P[+-]) (?P[^#]*) # (?P.*)z9> {seq_name}:{start}-{end} {strand} {file} # {ugly_hack} cCsP|jd\}}}tt|jd\}}|d8}||||fS)zDReturn (name, start, end) string tuple from an identifier (PRIVATE).:-r)splitmapint)Z identifieridlocstrandstartendr8/tmp/pip-build-ww9dw3qa/biopython/Bio/AlignIO/MauveIO.py_identifier_splitcs rcsCeZdZdZfddZddZdddZS) MauveWriterzMauve/XMFA alignment writer.cs/tt|j||d|_d|_dS)z Initialize.FN)superr__init__ _wrote_header _wrote_first)selfargskwargs) __class__rrrns zMauveWriter.__init__cCst|}|j|_|dkr3td|jdkrNtd|jsd|_|jjdx5td|dD] }|jjd||fqWx-t|D]\}}|j |d|qW|jjd 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#Sequence%sEntry %s record_idxz= N) lenZget_alignment_length_length_of_sequences ValueErrorrhandlewriterange enumerate _write_record)r alignmentcountiidxrecordrrrwrite_alignmentts      zMauveWriter.write_alignmentrc Cs |jt|jkr$td|j}ytt|j}Wn"tk rjt|d}YnXd|jkrId|jkrIdt|jdt|jdf}dt|jddt|jdf}|t| d|kr|dt| }|t| d|krI|dt| }d|jkrd|jkrd|jkrtj d|d|jddd|jdd|jddkrd nd d |jd d |j }d}n@tj d|dddddd d |jd d |j }d}d|ks<d|kr| r|j sd|_ tj d|dddddd d |jd d |j }|j j |dna|j j |xNtdt|jdD]1}|j j dt|j||dqWdS)z/Write a single SeqRecord to the file (PRIVATE).z%Sequences must all be the same lengthrrrz/%s-%sNrseq_name+r filez.faZ ugly_hackFrTz:0-0 z:1-0  Pz%s )r!r seqr"namestrr annotations ID_LINE_FMTformatrrr#r$r%) rr,rr.Zsuffix0Zsuffix1Zid_lineZlacking_annotationsr*rrrr'sf                "zMauveWriter._write_record)__name__ __module__ __qualname____doc__rr-r'rr)rrrks  !rc@s(eZdZdZgZddZdS) MauveIteratorzMauve xmfa alignment iterator.c CsN|j}|j}|s!tx+|rN|jjdrN|j}q$Wi}i}d}d}x|sqP|j}|jdrPn[|jdrtj|}|stj|}|std||j d}i} xdD]~} yc|j | } | dkr:t | } | d kr:| d8} | d krRt | } | | | zMalformed header line: %srrrrr4realnamerrz#Saw sequence before definition liner z8Sequences have different lengths, or repeated identifierz/{start}-{end}r/)zstartzendzidzstrandznamerA)r#readline StopIterationstrip startswithXMFA_HEADER_REGEX_BIOPYTHONmatchXMFA_HEADER_REGEXr"groupr IndexError_idsappend setdefaultAssertionErrorr ids sequencesmaxr listvaluesr8r)rrZalphabetr6r)rr#lineZseqsZ seq_regionsZpassed_end_alignmentZ latest_idmZ parsed_idZ parsed_datakeyvalueZalignment_lengthrecordsrr3suffixZ corrected_idr,rrr__next__s                 !  !8    ( $'zMauveIterator.__next__N)r9r:r;r<rMr\rrrrr=s r=)r< __future__rreZBio.SeqrZ Bio.SeqRecordrZ Bio.AlignrZ InterfacesrrcompilerJrHr7rrr=rrrrNs    z