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src/c/g/cgat-HEAD/CGAT/Mali.py   cgat(Download)
    '''
 
    import alignlib_lite
    m = alignlib_lite.py_makeMultipleAlignment()
    for identifier in mali.getIdentifiers():
                identifiers[x], a.getFrom(), a.getTo(), a.getString())
    else:
        import alignlib_lite
        output = alignlib_lite.py_MultAlignmentFormatPlain(mali, seqs)
        for x in range(mali.getNumSequences()):

src/c/g/cgat-HEAD/scripts/optic/regions2predictions.py   cgat(Download)
import CGAT.PredictionParser as PredictionParser
import CGAT.PredictionFile as PredictionFile
import alignlib_lite
 
param_loglevel = 2

src/c/g/cgat-HEAD/scripts/optic/regions2graph.py   cgat(Download)
import CGAT.PredictionParser as PredictionParser
import CGAT.PredictionFile as PredictionFile
import alignlib_lite
 
 

src/c/g/cgat-HEAD/scripts/optic/orthologs2transcripts.py   cgat(Download)
import CGAT.Genomics as Genomics
import CGAT.Exons as Exons
import alignlib_lite
 
import CGAT.WrapperDialign as WrapperDialign

src/c/g/cgat-HEAD/scripts/optic/links2exons.py   cgat(Download)
import CGAT.Genomics as Genomics
import CGAT.Exons as Exons
import alignlib_lite
import CGAT.BlastAlignments as BlastAlignments
 

src/c/g/cgat-HEAD/scripts/optic/filter_paralogous_links.py   cgat(Download)
import CGAT.Genomics as Genomics
import CGAT.Exons as Exons
import alignlib_lite
import CGAT.BlastAlignments as BlastAlignments
 

src/c/g/cgat-HEAD/scripts/optic/evaluate_mali.py   cgat(Download)
import scipy
import CGAT.Exons as Exons
import alignlib_lite
import CGAT.Genomics as Genomics
import numpy

src/c/g/cgat-HEAD/scripts/optic/cds2codons.py   cgat(Download)
import CGAT.Experiment as E
import CGAT.Genomics as Genomics
import alignlib_lite
 
 

src/c/g/cgat-HEAD/scripts/optic/analyze_orthology_pairwise.py   cgat(Download)
import numpy
import CGAT.Histogram as Histogram
import alignlib_lite
import CGAT.AlignedPairs as AlignedPairs
import CGAT.TreeTools as TreeTools

src/c/g/cgat-HEAD/scripts/optic/analyze_orthology.py   cgat(Download)
import numpy
import CGAT.Histogram as Histogram
import alignlib_lite
import CGAT.AlignedPairs as AlignedPairs
import CGAT.TreeTools as TreeTools

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