ó ˆé¯Ic@sldZddlmZddlmZddlmZdfd„ƒYZd„Ze dkrheƒnd S( s† Contains classes to deal with generic sequence alignment stuff not specific to a particular program or format. classes: o Alignment iÿÿÿÿ(tSeq(t SeqRecord(tAlphabett AlignmentcBs•eZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d „Z d „Z ddd d „Zd„Zd„ZRS(s¢Represent a set of alignments. This is a base class to represent alignments, which can be subclassed to deal with an alignment in a specific format. cCsIt|tjƒp!t|tjƒs3tdƒ‚n||_g|_dS(s£Initialize a new Alignment object. Arguments: o alphabet - The alphabet to use for the sequence objects that are created. This alphabet must be a gapped type. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> print align Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACT-CTAGCTAG Beta ACTGCTAGATAG Gamma sInvalid alphabet argumentN(t isinstanceRtAlphabetEncodert ValueErrort _alphabett_records(tselftalphabet((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt__init__s  cCsOt|jƒdkr)d|j|jfSd|jd |jd|jfSdS(sŒReturns a truncated string representation of a SeqRecord (PRIVATE). This is a PRIVATE function used by the __str__ method. i2s%s %ss %s...%s %si,iýÿÿÿN(tlentseqtid(R trecord((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt _str_line5scCsÖt|jƒ}dt|jƒ||jƒfg}|dkro|jg|jD]}|j|ƒ^qPƒnZ|jg|jd D]}|j|ƒ^qƒƒ|jdƒ|j|j|jdƒƒdj|ƒS(sCReturns a multi-line string summary of the alignment. This output is intended to be readable, but large alignments are shown truncated. A maximum of 20 rows (sequences) and 50 columns are shown, with the record identifiers. This should fit nicely on a single screen. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> print align Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACT-CTAGCTAG Beta ACTGCTAGATAG Gamma See also the alignment's format method. s(%s alignment with %i rows and %i columnsiis...iÿÿÿÿs ( R RtstrRtget_alignment_lengthtextendRtappendtjoin(R trowstlinestrec((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt__str__@s" /0 cCs8d|jt|jƒ|jƒt|jƒt|ƒfS(s÷Returns a representation of the object for debugging. The representation cannot be used with eval() to recreate the object, which is usually possible with simple python ojects. For example: The hex string is the memory address of the object, see help(id). This provides a simple way to visually distinguish alignments of the same size. s1<%s instance (%i records of length %i, %s) at %x>(t __class__R RRtreprRR(R ((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt__repr__`scCs |j|ƒS(sûReturns the alignment as a string in the specified file format. The format should be a lower case string supported as an output format by Bio.AlignIO (such as "fasta", "clustal", "phylip", "stockholm", etc), which is used to turn the alignment into a string. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> print align.format("fasta") >Alpha ACTGCTAGCTAG >Beta ACT-CTAGCTAG >Gamma ACTGCTAGATAG >>> print align.format("phylip") 3 12 Alpha ACTGCTAGCT AG Beta ACT-CTAGCT AG Gamma ACTGCTAGAT AG For Python 2.6, 3.0 or later see also the built in format() function. (t __format__(R tformat((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyRws!cCs]|rOddlm}ddlm}|ƒ}|j|g||ƒ|jƒSt|ƒSdS(s7Returns the alignment as a string in the specified file format. This method supports the python format() function added in Python 2.6/3.0. The format_spec should be a lower case string supported by Bio.AlignIO as an output file format. See also the alignment's format() method.iÿÿÿÿ(tStringIO(tAlignION(RtBioR twritetgetvalueR(R t format_specRR thandle((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyR›s  cCs|jS(sFReturn all of the sequences involved in the alignment. The return value is a list of SeqRecord objects. This method is semi-obsolete, as the Alignment object itself offers much of the functionality of a list of SeqRecord objects (e.g. iteration or slicing to create a sub-alignment). (R(R ((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt get_all_seqs¬s cCs t|jƒS(s.Iterate over alignment rows as SeqRecord objects. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> for record in align : ... print record.id ... print record.seq Alpha ACTGCTAGCTAG Beta ACT-CTAGCTAG Gamma ACTGCTAGATAG (titerR(R ((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt__iter__·scCs|j|jS(sHRetrieve a sequence by row number (OBSOLETE). Returns: o A Seq object for the requested sequence. Raises: o IndexError - If the specified number is out of range. NOTE: This is a legacy method. In new code where you need to access the rows of the alignment (i.e. the sequences) consider iterating over them or accessing them as SeqRecord objects. e.g. for record in alignment : print record.id print record.seq first_record = alignment[0] last_record = alignment[-1] (RR (R tnumber((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pytget_seq_by_numÌscCs t|jƒS(s€Returns the number of sequences in the alignment. Use len(alignment) to get the number of sequences (i.e. the number of rows), and alignment.get_alignment_length() to get the length of the longest sequence (i.e. the number of columns). This is easy to remember if you think of the alignment as being like a list of SeqRecord objects. (R R(R ((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt__len__ás cCsEd}x8|jD]-}t|jƒ|krt|jƒ}qqW|S(sçReturn the maximum length of the alignment. All objects in the alignment should (hopefully) have the same length. This function will go through and find this length by finding the maximum length of sequences in the alignment. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> align.get_alignment_length() 12 If you want to know the number of sequences in the alignment, use len(align) instead: >>> len(align) 3 i(RR R (R t max_lengthR((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyRís gð?cCswt||jƒ}t|d|d|ƒ}|r@||jd no weight, 1.0 => highest weight) Rt descriptiontstarttendtweightN(RRRt annotationsRR(R t descriptortsequenceR.R/R0tnew_seqt new_record((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt add_sequence s   cCsSd}|dkr$||jƒks*t‚x"|jD]}||j|7}q4W|S(s»Returns a string containing a given column. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> align.get_column(0) 'AAA' >>> align.get_column(3) 'G-G' ti(RtAssertionErrorRR (R tcoltcol_strR((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt get_column>s $cCst|tƒr|j|St|tƒrLt|jƒ}|j||_|St|ƒdkrqtddƒ‚n tdƒ‚dS(szAccess part of the alignment. We'll use the following example alignment here for illustration: >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> align.add_sequence("Delta", "ACTGCTTGCTAG") >>> align.add_sequence("Epsilon","ACTGCTTGATAG") You can access a row of the alignment as a SeqRecord using an integer index (think of the alignment as a list of SeqRecord objects here): >>> first_record = align[0] >>> print first_record.id, first_record.seq Alpha ACTGCTAGCTAG >>> last_record = align[-1] >>> print last_record.id, last_record.seq Epsilon ACTGCTTGATAG You can also access use python's slice notation to create a sub-alignment containing only some of the SeqRecord objects: >>> sub_alignment = align[2:5] >>> print sub_alignment Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGATAG Gamma ACTGCTTGCTAG Delta ACTGCTTGATAG Epsilon This includes support for a step, i.e. align[start:end:step], which can be used to select every second sequence: >>> sub_alignment = align[::2] >>> print sub_alignment Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACTGCTAGATAG Gamma ACTGCTTGATAG Epsilon Or to get a copy of the alignment with the rows in reverse order: >>> rev_alignment = align[::-1] >>> print rev_alignment Gapped(IUPACUnambiguousDNA(), '-') alignment with 5 rows and 12 columns ACTGCTTGATAG Epsilon ACTGCTTGCTAG Delta ACTGCTAGATAG Gamma ACT-CTAGCTAG Beta ACTGCTAGCTAG Alpha Right now, these are the ONLY indexing operations supported. The use of a second column based index is under discussion for a future update. is3Row and Column indexing is not currently supported,sbut may be in future.sInvalid index type.N(RtintRtsliceRRR t TypeError(R tindext sub_align((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt __getitem__Ss9  N(t__name__t __module__t__doc__R RRRRRR&R(R*R+RtNoneR6R;RA(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyRs    $     2 cCs$dGHddl}|jƒdGHdS(s"Run the Bio.Seq module's doctests.sRunning doctests...iÿÿÿÿNtDone(tdoctestttestmod(RG((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pyt_testžs  t__main__N( RDtBio.SeqRt Bio.SeqRecordRR!RRRIRB(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Align/Generic.pytsÿŠ