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@@ -61,7 +61,7 @@ |
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dAlnCov = {} |
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llhFile = inDir+"/DGINN_{}_likelihoods.tab".format(timeStamp) |
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llh = open(llhFile, "w") |
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llh.write("File\tMethod\tM1\tM2\tM7\tM8\n") |
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llh.write("File\tMethod\tM1\tM2\tM7\tM8\tDFP07_0\tDFP07\n") |
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for posDir, aln in dSub2Cut.items(): |
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#posDir = "/home/lea/Documents/genes/2020_shScreen/TRIM69_CCDS_results_202004012008/TRIM69_sequences_filtered_longestORFs_mafft_mincov_prank_results_202004201724/positive_selection_results_202004201724/" |
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@@ -95,9 +95,10 @@ |
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dGene.update(bust) |
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meme = PRS.ResMeme(baseName, posDir) |
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dGene.update(meme) |
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bpp1v2, bpp7v8, bppLlh = PRS.ResBpp(baseName, posDir, pr) |
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bpp1v2, bpp7v8, bppdfp, bppLlh = PRS.ResBpp(baseName, posDir, pr) |
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dGene.update(bpp1v2) |
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dGene.update(bpp7v8) |
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dGene.update(bppdfp) |
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paml1v2, paml7v8, pamlLlh = PRS.ResPaml(posDir, pr) |
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dGene.update(paml1v2) |
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dGene.update(paml7v8) |
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@@ -139,12 +140,12 @@ |
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resLine = "\t".join(lBaseRes + list(dGene.values())) |
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allRes.append(resLine) |
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bppLlhRes = [str(bppLlh[k]) for k in ["M1","M2","M7","M8"]] |
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bppLlhRes = [str(bppLlh[k]) for k in ["M1","M2","M7","M8","DFP07_0","DFP07"]] |
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llh.write(baseName+"\tBPP\t"+"\t".join(bppLlhRes)+"\n") |
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if type(bppLlh) is dict: |
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pamlLlhRes = [str(value) for value in pamlLlh.values()] |
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llh.write(baseName+"\tPAML\t"+"\t".join(pamlLlhRes)+"\n") |
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llh.write(baseName+"\tPAML\t"+"\t".join(pamlLlhRes)+2*"\tna"+"\n") |
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else: |
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llh.write(baseName+"\tPAML\tna\n") |
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