minorg.mafftcommandline_add module

Command line wrapper for the multiple alignment programme MAFFT, modified to include --add option.

class minorg.mafftcommandline_add.MafftCommandline(cmd='mafft', **kwargs)

Bases: Bio.Application.AbstractCommandline

Command line wrapper for the multiple alignment program MAFFT. http://align.bmr.kyushu-u.ac.jp/mafft/software/ .. rubric:: Notes

Last checked against version: MAFFT v6.717b (2009/12/03)

References

Katoh, Toh (BMC Bioinformatics 9:212, 2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (describes RNA structural alignment methods) Katoh, Toh (Briefings in Bioinformatics 9:286-298, 2008) Recent developments in the MAFFT multiple sequence alignment program (outlines version 6) Katoh, Toh (Bioinformatics 23:372-374, 2007) Errata PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm) Katoh, Kuma, Toh, Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies) Katoh, Misawa, Kuma, Miyata (Nucleic Acids Res. 30:3059-3066, 2002)

Examples

>>> from Bio.Align.Applications import MafftCommandline
>>> mafft_exe = "/opt/local/mafft"
>>> in_file = "../Doc/examples/opuntia.fasta"
>>> mafft_cline = MafftCommandline(mafft_exe, input=in_file)
>>> print(mafft_cline)
/opt/local/mafft ../Doc/examples/opuntia.fasta
If the mafft binary is on the path (typically the case on a Unix style
operating system) then you don't need to supply the executable location:
>>> from Bio.Align.Applications import MafftCommandline
>>> in_file = "../Doc/examples/opuntia.fasta"
>>> mafft_cline = MafftCommandline(input=in_file)
>>> print(mafft_cline)
mafft ../Doc/examples/opuntia.fasta
You would typically run the command line with mafft_cline() or via
the Python subprocess module, as described in the Biopython tutorial.
Note that MAFFT will write the alignment to stdout, which you may
want to save to a file and then parse, e.g.::
    stdout, stderr = mafft_cline()
    with open("aligned.fasta", "w") as handle:
        handle.write(stdout)
    from Bio import AlignIO
    align = AlignIO.read("aligned.fasta", "fasta")
Alternatively, to parse the output with AlignIO directly you can
use StringIO to turn the string into a handle::
    stdout, stderr = mafft_cline()
    from io import StringIO
    from Bio import AlignIO
    align = AlignIO.read(StringIO(stdout), "fasta")

__init__(cmd='mafft', **kwargs)

Initialize the class.