Exemple #1
0
def name(fN):
        

if __name__ == "__main__":
        import sys
        if sys.argv[1] == "help":
                bioLibCG.gd(sys.argv[0])
        else:
                bioLibCG.submitArgs(globals()[sys.argv[1]], sys.argv[1:])
Exemple #2
0
    #fracs = pieFractions(counts)
    plots_labels = [[], []]
    for con in context_level_count:
        x = []
        y = []
        sortedLevs = sorted(context_level_count[con].keys())
        for lev in sortedLevs:
            x.append(lev)
            y.append(context_level_count[con][lev])
        plots_labels[0].append(plt.plot(
            x,
            y,
        ))
        plots_labels[1].append(con)

    #plot
    plt.legend(plots_labels[0], plots_labels[1])
    plt.title(
        'oRNA Targets\' Context Proportion Stability w/ Expression Increase')
    plt.xlabel('Degradome Expression Cutoff')
    plt.ylabel('Number of oRNA Targets')
    plt.show()


if __name__ == "__main__":
    import sys
    if sys.argv[1] == "help":
        bioLibCG.gd(sys.argv[0])
    else:
        bioLibCG.submitArgs(globals()[sys.argv[1]], sys.argv[1:])
                #3UTR
                if strand == '1':
                        if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
                                p.tell('3 is none')
                                c += 1 
                                if codingStatus:
                                        e += 1
                                range3 = ()
                        else:
                                range3 = (cEnd + 1, tEnd)
                else:
                        if cStart == tStart or cStart == tEnd + 1:
                                p.tell('3 is none')
                                c += 1
                                if codingStatus:
                                        e += 1
                                range3 = ()
                        else:
                                range3 = (tStart, cStart - 1)

                a += 1

        print a, b, c, d, e                

if __name__ == "__main__":
        import sys
        if sys.argv[1] == "help":
                bioLibCG.gd(sys.argv[0])
        else:
                bioLibCG.submitArgs(globals()[sys.argv[1]], sys.argv[1:])
        'tRNA_pseudogene_noncoding',
        'pseudogene_noncoding',
        'protein_coding',
        'None']


        ds = cg.dominantSpotter(domOrder)


        for oID in oNX.tcc:

                oChrom, oStrand, start, end = cg.tccSplit(oNX.tcc[oID])
                if oChrom == chrom and oStrand == strand:

                        tranTypes = coord_types.get(start, 'None').split(',')
                        types = [x.split(':')[1] if x != 'None' else 'None' for x in tranTypes]

                        types = list(set(types))
                        oNX.transcriptTypes[oID] = types 
                        oNX.transcriptType[oID] = ds.spotItem(types)

        
        oNX.save()

if __name__ == "__main__":
	import sys
        if sys.argv[1] == 'help':
                cg.gd(sys.argv[0])
        else:
                cg.submitArgs(globals()[sys.argv[1]], sys.argv[1:])
        'tRNA_pseudogene_noncoding',
        'pseudogene_noncoding',
        'protein_coding',
        'None']


        ds = cg.dominantSpotter(domOrder)


        for oID in oNX.tcc:

                oChrom, oStrand, start, end = cg.tccSplit(oNX.tcc[oID])
                if oChrom == chrom and oStrand == strand:

                        tranTypes = coord_types.get(start, 'None').split(',')
                        types = [x.split(':')[1] if x != 'None' else 'None' for x in tranTypes]

                        types = list(set(types))
                        oNX.transcriptTypes[oID] = types 
                        oNX.transcriptType[oID] = ds.spotItem(types)

        
        oNX.save()

if __name__ == "__main__":
	import sys
        if sys.argv[1] == 'help':
                cg.gd(sys.argv[0])
        else:
                cg.submitArgs(globals()[sys.argv[1]], sys.argv[1:])