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@@ -41,12 +41,12 @@ def pspAnalysis(data, parms, aln, tree): |
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logger.info("Analysis to be run:") |
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dAnalysis = {"paml": "Site (codeml)", |
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"BUSTED":"Whole-Gene", |
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"bppml":"Site (Bio++ - Optimization)", |
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"bppmixedlikelihood":"Site (Bio++ - Results)", |
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"OPB":"Branch", |
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"GNH":"Branch-site on positively selected branches", |
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"MEME":"Branch-site"} |
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"BUSTED":"Whole-Gene", |
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"bppml":"Site (Bio++ - Optimization)", |
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"bppmixedlikelihood":"Site (Bio++ - Results)", |
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"OPB":"Branch", |
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"GNH":"Branch-site on positively selected branches", |
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"MEME":"Branch-site"} |
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for key in dCtrls.keys(): |
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logger.info(dAnalysis[key]) |
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@@ -60,42 +60,39 @@ def pspAnalysis(data, parms, aln, tree): |
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if "MEME" in dCtrls: |
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try: |
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BranchAnalysis.memeBranchSite(aln, |
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cladoFile, |
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outDir, |
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data.baseName, |
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logger) |
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cladoFile, |
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outDir, |
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data.baseName, |
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logger) |
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except Exception: |
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logger.error("MEME encountered an unexpected error, skipping.") |
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if "bppml" and "bppmixedlikelihood" in dCtrls and len(lModels) > 1: |
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#try: |
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SiteAnalysis.bppSite(dCtrls["bppml"], |
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dCtrls["bppmixedlikelihood"], |
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aln, |
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data.alnFormat, |
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tree, |
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lModels, |
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outDir, |
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data.baseName, |
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logger) |
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#except Exception: |
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#logger.error("Bio++ Site encountered an unexpected error, skipping.") |
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elif "bppml" or "bppmixedlikelihood" not in dCtrls: |
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logger.error("Part of parameters for Bio++ site analysis are completed but not all.") |
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logger.error("Analysis ignored (if unexpected, check paths to Bio++/bpp parameter files).") |
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elif "bppml" and "bppmixedlikelihood" not in dCtrls: |
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next |
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if "bppml" in dCtrls: |
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# try: |
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if not dCtrls["bppmixedlikelihood"]: |
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dCtrls["bppmixedlikelihood"]=dCtrls["bppml"] |
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SiteAnalysis.bppSite(dCtrls["bppml"], |
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dCtrls["bppmixedlikelihood"], |
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aln, |
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data.alnFormat, |
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tree, |
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lModels, |
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outDir, |
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data.baseName, |
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logger) |
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# except Exception: |
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# logger.error("Bio++ Site encountered an unexpected error, skipping.") |
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lPSNodes = [] |
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if "OPB" in dCtrls: |
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try: |
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params = BranchAnalysis.bppBranch(dCtrls["OPB"], |
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outDir, |
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data.baseName, |
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aln, |
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data.alnFormat, |
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tree, |
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logger) |
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outDir, |
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data.baseName, |
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aln, |
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data.alnFormat, |
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tree, |
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logger) |
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except Exception: |
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logger.error("Bio++ Branch Analysis encountered an unexpected error, skipping.") |
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try: |
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@@ -109,14 +106,14 @@ def pspAnalysis(data, parms, aln, tree): |
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except Exception: |
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logger.error("Bio++ Pseudo Branch-Site Analysis encountered an unexpected error, skipping.") |
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if "paml" in dCtrls and dCtrls["paml"] not in ["False", False] and len(lModels) > 1: |
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if "paml" in dCtrls: |
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SiteAnalysis.pamlSite(aln, |
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tree, |
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lModels, |
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dCtrls["paml"], |
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outDir, |
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data.baseName, |
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logger) |
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tree, |
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lModels, |
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dCtrls["paml"], |
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outDir, |
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data.baseName, |
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logger) |
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"""try: |
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SiteAnalysis.pamlSite(aln, tree, lModels, dCtrls["paml"], outDir, data.baseName, logger) |
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except Exception: |
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