ó ¾xÂIc@s{dZddlmZddlmZmZdefd„ƒYZdefd„ƒYZd„Ze d krweƒnd S( s  Bio.AlignIO support for the "stockholm" format (used in the PFAM database). 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 Stockholm alignment file containing the following: # STOCKHOLM 1.0 #=GC SS_cons .................<<<<<<<<...<<<<<<<........>>>>>>>.. AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGU #=GR AP001509.1 SS -----------------<<<<<<<<---..<<-<<-------->>->>..-- AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGU #=GR AE007476.1 SS -----------------<<<<<<<<-----<<.<<-------->>.>>---- #=GC SS_cons ......<<<<<<<.......>>>>>>>..>>>>>>>>............... AP001509.1 CUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU #=GR AP001509.1 SS -------<<<<<--------->>>>>--->>>>>>>>--------------- AE007476.1 UUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU #=GR AE007476.1 SS ------.<<<<<--------->>>>>.-->>>>>>>>--------------- // This is a single multiple sequence alignment, so you would probably load this using the Bio.AlignIO.read() function: >>> from Bio import AlignIO >>> handle = open("Stockholm/simple.sth", "rU") >>> align = AlignIO.read(handle, "stockholm") >>> handle.close() >>> print align SingleLetterAlphabet() alignment with 2 rows and 104 columns UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-G...UGU AP001509.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-C...GAU AE007476.1 >>> for record in align : ... print record.id, len(record) AP001509.1 104 AE007476.1 104 This example file is clearly using RNA, so you might want the Alignment object (and the SeqRecord objects it holds) to reflect this, rather than simple using the default single letter alphabet as shown above. You can do this with an optional argument to the Bio.AlignIO.read() function: >>> from Bio import AlignIO >>> from Bio.Alphabet import generic_rna >>> handle = open("Stockholm/simple.sth", "rU") >>> align = AlignIO.read(handle, "stockholm", alphabet=generic_rna) >>> handle.close() >>> print align RNAAlphabet() alignment with 2 rows and 104 columns UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-G...UGU AP001509.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-C...GAU AE007476.1 In addition to the sequences themselves, this example alignment also includes some GR lines for the secondary structure of the sequences. These are strings, with one character for each letter in the associated sequence: >>> for record in align : ... print record.id ... print record.seq ... print record.letter_annotations['secondary_structure'] AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>--------------- AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>--------------- Any general annotation for each row is recorded in the SeqRecord's annotations dictionary. You can output this alignment in many different file formats using Bio.AlignIO.write(), or the Alignment object's format method: >>> print align.format("fasta") >AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-A GGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU >AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAA GGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU Most output formats won't be able to hold the annotation possible in a Stockholm file: >>> print align.format("stockholm") # STOCKHOLM 1.0 #=GF SQ 2 AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU #=GS AP001509.1 AC AP001509.1 #=GS AP001509.1 DE AP001509.1 #=GR AP001509.1 SS -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>--------------- AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU #=GS AE007476.1 AC AE007476.1 #=GS AE007476.1 DE AE007476.1 #=GR AE007476.1 SS -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>--------------- // Note that when writing Stockholm files, Biopython does not break long sequences up and interleave them (as in the input file shown above). The standard allows this simpler layout, and it is more likely to be understood by other tools. Finally, as an aside, it can sometimes be useful to use Bio.SeqIO.parse() to iterate over the two rows as SeqRecord objects - rather than working with Alignnment objects. Again, if you want to you can specify this is RNA: >>> from Bio import SeqIO >>> from Bio.Alphabet import generic_rna >>> handle = open("Stockholm/simple.sth", "rU") >>> for record in SeqIO.parse(handle, "stockholm", alphabet=generic_rna) : ... print record.id ... print record.seq ... print record.letter_annotations['secondary_structure'] AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>--------------- AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>--------------- >>> handle.close() iÿÿÿÿ(t Alignment(tAlignmentIteratortSequentialAlignmentWritertStockholmWritercBsreZdZidd6dd6dd6dd6d d 6d d 6d d6Zidd6dd6dd6Zd„Zd„ZRS(s Stockholm/PFAM alignment writer.tSStsecondary_structuretSAtsurface_accessibilitytTMt transmembranetPPtposterior_probabilitytLItligand_bindingtASt active_sitetINtintrontOStorganismtOCtorganism_classificationtLOtlookcCs¿|jƒ}t|ƒ}|jƒ|_g|_|dkrKtdƒ‚n|jdkritdƒ‚n|jjdƒ|jjd|ƒx|D]}|j|ƒq”W|jjdƒdS(sûUse 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). isMust have at least one sequences Non-empty sequences are requireds# STOCKHOLM 1.0 s #=GF SQ %i s// N( t get_all_seqstlentget_alignment_lengtht_length_of_sequencest _ids_writtent ValueErrorthandletwritet _write_record(tselft alignmenttrecordstcounttrecord((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/StockholmIO.pytwrite_alignment’s     cCsG|jt|jƒkr'tdƒ‚n|j}|jdk rvd|jkrv|j|jdkrs|j}qsqvn|jddƒ}d|jkrd|jkrdt |jdƒt |jdƒf}|t|ƒ |krd|t |jdƒt |jdƒf}qn||j kr<td |ƒ‚n|j j |ƒ|j j d ||jjƒfƒd|jkr«|j j d ||j|jdƒfƒn2|jrÝ|j j d ||j|jƒfƒn|jr|j j d ||j|jƒfƒnx4|jD])}|j j d ||j|ƒfƒqWxk|jjƒD]Z\}}||jkrV|j j d||j|j|ƒ|jt |ƒƒfƒqVqVWxŒ|jjƒD]{\}}||jkrÄtt |ƒƒt|jƒkrÄ|j j d||j|j|ƒ|jt |ƒƒfƒqÄqÄWdS(s$Write a single SeqRecord to the files%Sequences must all be the same lengtht accessiont t_tstarttends/%s-%ss%s/%s-%ssDuplicate record identifier: %ss%s %s s#=GS %s AC %s s#=GS %s DE %s s#=GS %s DR %s s#=GS %s %s %s s#=GR %s %s %s N(RRtseqRtidtnametNonet annotationstreplacetstrRtappendRRttostringtcleant descriptiontdbxrefst iteritemstpfam_gs_mappingtletter_annotationstpfam_gr_mapping(R!R%tseq_nametsuffixtxreftkeytvalue((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/StockholmIO.pyR ­s\ # !      0 (t__name__t __module__t__doc__R;R9R&R (((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/StockholmIO.pyRs     tStockholmIteratorcBs„eZdZidd6dd6dd6dd6d d 6d d 6d d6Zidd6dd6dd6Zd„Zd„Zd„Zd„ZRS(s Loads a Stockholm file from PFAM into Alignment objects. The file may contain multiple concatenated alignments, which are loaded and returned incrementally. This parser will detect if the Stockholm file follows the PFAM conventions for sequence specific meta-data (lines starting #=GS and #=GR) and populates the SeqRecord fields accordingly. Any annotation which does not follow the PFAM conventions is currently ignored. If an accession is provided for an entry in the meta data, IT WILL NOT be used as the record.id (it will be recorded in the record's annotations). This is because some files have (sub) sequences from different parts of the same accession (differentiated by different start-end positions). Wrap-around alignments are not supported - each sequences must be on a single line. However, interlaced sequences should work. For more information on the file format, please see: http://www.bioperl.org/wiki/Stockholm_multiple_alignment_format http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html For consistency with BioPerl and EMBOSS we call this the "stockholm" format. RRRRR RR R R R RRRRRRRRRRcCsy|j}|`Wn tk r5|jjƒ}nX|s@dS|jƒdksatdƒ‚ni}g}i}i}i}t}xÎ|jjƒ}|s¡Pn|jƒ}|dkrÆ||_Pqˆ|dkrÛt}qˆ|dkrêqˆ|ddkr²| st‚g|j ddƒD]}|jƒ^q} t | ƒd kr[td d |ƒ‚n| \} } | |krƒ|j | ƒn|j | dƒ|| c| j d d ƒ7}s~ÿ