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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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