B b[4@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)Z identifieridZlocstrandstartendr2lib/python3.7/site-packages/Bio/AlignIO/MauveIO.py_identifier_splitbsrcs2eZdZdZfddZddZd ddZZS) MauveWriterzMauve/XMFA alignment writer.cstj||d|_d|_dS)zInitialize the class.FN)super__init__ _wrote_header _wrote_first)selfargskwargs) __class__rrrmszMauveWriter.__init__cCst|}||_|dkr"td|jdkr4td|jsxd|_|jdx*td|dD]}|jd||fq\Wx"t|D]\}}|j ||dqW|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#Sequence%sEntry %s ) record_idxz= N) lenZget_alignment_length_length_of_sequences ValueErrorrhandlewriterange enumerate _write_record)rZ alignmentcountiidxrecordrrrwrite_alignmentss   zMauveWriter.write_alignmentrc CsH|jt|jkrtd|j}ytt|j}Wn tk rPt|d}YnXd|jkrd|jkrd|jd|jdf}d|jdd|jdf}|t| d|kr|dt| }|t| d|kr|dt| }d|jkrVd|jkrVd|jkrVtj ||jdd|jd|jddkrzMalformed header line: %sr )rrr rr3realnamerrrrz#Saw sequence before definition liner z8Sequences have different lengths, or repeated identifierz/{start}-{end}rBr3)r r3rr+)r!readline StopIterationstrip startswithXMFA_HEADER_REGEX_BIOPYTHONmatchXMFA_HEADER_REGEXr groupr IndexError_idsappend setdefaultAssertionErrorrZids sequencesmaxr listvaluesr7r&rrr5r)rr!lineZseqsZ seq_regionsZpassed_end_alignmentZ latest_idmZ parsed_idZ parsed_datakeyvalueZalignment_lengthZrecordsr r2suffixZ corrected_idr)rrr__next__s                 .  $    zMauveIterator.__next__N)r9r:r;r<rNr[rrrrr>sr>)r<reZ Bio.AlignrZBio.SeqrZ Bio.SeqRecordrZ InterfacesrrcompilerKrIr6rrr>rrrrNs     {