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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.
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Returns 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. |
Access part of the alignment. 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 = my_alignment[0] last_record = my_alignment[-1] You can also access use python's slice notation to create a sub-alignment containing only some of the SeqRecord objects: sub_alignment = my_alignment[2:20] This includes support for a step, sub_alignment = my_alignment[start:end:step] For example to select every second sequence: sub_alignment = my_alignment[::2] Or to reverse the row order: rev_alignment = my_alignment[::-1] Right now, these are the ONLY indexing operations supported. The use of a second column based index is under discussion for a future update. |
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", "ACTGCTAGDTAG") >>> print align Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACT-CTAGCTAG Beta ACTGCTAGDTAG Gamma |
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", "ACTGCTAGDTAG") >>> for record in align : ... print record.id ... print record.seq Alpha ACTGCTAGCTAG Beta ACT-CTAGCTAG Gamma ACTGCTAGDTAG |
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: <Bio.Align.Generic.Alignment instance (2 records of length 14, SingleLetterAlphabet()) at a3c184c> 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. |
Returns 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", "ACTGCTAGDTAG") >>> print align Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACT-CTAGCTAG Beta ACTGCTAGDTAG Gamma See also the alignment's format method. |
Returns a truncated string representation of a SeqRecord (PRIVATE). This is a PRIVATE function used by the __str__ method. |
Add a sequence to the alignment. This doesn't do any kind of alignment, it just adds in the sequence object, which is assumed to be prealigned with the existing sequences. Arguments: o descriptor - The descriptive id of the sequence being added. This will be used as the resulting SeqRecord's .id property (and, for historical compatibility, also the .description property) o sequence - A string with sequence info. o start - You can explicitly set the start point of the sequence. This is useful (at least) for BLAST alignments, which can just be partial alignments of sequences. o end - Specify the end of the sequence, which is important for the same reason as the start. o weight - The weight to place on the sequence in the alignment. By default, all sequences have the same weight. (0.0 => no weight, 1.0 => highest weight) |
Returns 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", "ACTGCTAGDTAG") >>> print align.format("fasta") >Alpha ACTGCTAGCTAG >Beta ACT-CTAGCTAG >Gamma ACTGCTAGDTAG <BLANKLINE> >>> print align.format("phylip") 3 12 Alpha ACTGCTAGCT AG Beta ACT-CTAGCT AG Gamma ACTGCTAGDT AG <BLANKLINE> For Python 2.6, 3.0 or later see also the built in format() function. |
Return 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", "ACTGCTAGDTAG") >>> align.get_alignment_length() 12 |
Return 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). |
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", "ACTGCTAGDTAG") >>> align.get_column(0) 'AAA' >>> align.get_column(3) 'G-G' |
Retrieve 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] |
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