Bio.AlignIO

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Multiple sequence alignment input/output as alignment objects.

The Bio.AlignIO interface is deliberately very similar to Bio.SeqIO, and in
fact the two are connected internally.  Both modules use the same set of file
format names (lower case strings).  From the user's perspective, you can read
in a PHYLIP file containing one or more alignments using Bio.AlignIO, or you
can read in the sequences within these alignmenta using Bio.SeqIO.

Bio.AlignIO is also documented at U{http://biopython.org/wiki/AlignIO} and by
a whole chapter in our tutorial:(more...)

src/b/i/biopython-1.63/Doc/examples/make_subsmat.py biopython(Download)

# Biopython
from Bio import SubsMat
from Bio import AlignIO
from Bio.Alphabet import IUPAC, Gapped
from Bio.Align import AlignInfo

src/b/i/biopython-HEAD/Doc/examples/make_subsmat.py biopython(Download)

# Biopython
from Bio import SubsMat
from Bio import AlignIO
from Bio.Alphabet import IUPAC, Gapped
from Bio.Align import AlignInfo

src/b/i/biopython-1.63/Doc/examples/clustal_run.py biopython(Download)

from Bio.Alphabet import Gapped, IUPAC
from Bio.Align.Applications import ClustalwCommandline
from Bio import AlignIO
from Bio.Align import AlignInfo
from Bio.SubsMat import FreqTable

src/b/i/biopython-HEAD/Doc/examples/clustal_run.py biopython(Download)

from Bio.Alphabet import Gapped, IUPAC
from Bio.Align.Applications import ClustalwCommandline
from Bio import AlignIO
from Bio.Align import AlignInfo
from Bio.SubsMat import FreqTable

src/p/h/phyloGenerator-HEAD/phyloGenerator.py phyloGenerator(Download)

from scipy import percentile,mean,std
import subprocess, threading #Background process class
from Bio import AlignIO #Handle alignments
from Bio.Align import MultipleSeqAlignment #Create an alignment (for MUSCLE)
import os #Remove temporary files

src/b/i/biopython-1.63/Bio/Align/Generic.py biopython(Download)

        if format_spec:
            from Bio._py3k import StringIO
            from Bio import AlignIO
            handle = StringIO()
            AlignIO.write([self], handle, format_spec)

src/b/i/biopython-1.63/Bio/Align/AlignInfo.py biopython(Download)

if __name__ == "__main__":
    print("Quick test")
    from Bio import AlignIO
    from Bio.Align.Generic import Alignment

src/b/i/biopython-HEAD/Bio/Align/Generic.py biopython(Download)

        if format_spec:
            from Bio._py3k import StringIO
            from Bio import AlignIO
            handle = StringIO()
            AlignIO.write([self], handle, format_spec)

src/b/i/biopython-HEAD/Bio/Align/AlignInfo.py biopython(Download)

if __name__ == "__main__":
    print("Quick test")
    from Bio import AlignIO
    from Bio.Align.Generic import Alignment

src/r/n/rnaseqlib-HEAD/rnaseqlib/motif/motif_clustering.py rnaseqlib(Download)

    from Bio.Alphabet import IUPAC
    import Bio.Seq as bio_seq
    import Bio.AlignIO as align_io
    # Load CLUSTALW file
    if not os.path.isfile(clustalw_fname):

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