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mgmt DFP07 in parse

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lgueguen committed Feb 22, 2021
1 parent 48e64bb commit ffe2fb56e441565274c4d07526f05d98b2e3105a
Showing with 5 additions and 4 deletions.
  1. +5 −4 etc/parseResults.py
@@ -61,7 +61,7 @@
dAlnCov = {}
llhFile = inDir+"/DGINN_{}_likelihoods.tab".format(timeStamp)
llh = open(llhFile, "w")
llh.write("File\tMethod\tM1\tM2\tM7\tM8\n")
llh.write("File\tMethod\tM1\tM2\tM7\tM8\tDFP07_0\tDFP07\n")

for posDir, aln in dSub2Cut.items():
#posDir = "/home/lea/Documents/genes/2020_shScreen/TRIM69_CCDS_results_202004012008/TRIM69_sequences_filtered_longestORFs_mafft_mincov_prank_results_202004201724/positive_selection_results_202004201724/"
@@ -95,9 +95,10 @@
dGene.update(bust)
meme = PRS.ResMeme(baseName, posDir)
dGene.update(meme)
bpp1v2, bpp7v8, bppLlh = PRS.ResBpp(baseName, posDir, pr)
bpp1v2, bpp7v8, bppdfp, bppLlh = PRS.ResBpp(baseName, posDir, pr)
dGene.update(bpp1v2)
dGene.update(bpp7v8)
dGene.update(bppdfp)
paml1v2, paml7v8, pamlLlh = PRS.ResPaml(posDir, pr)
dGene.update(paml1v2)
dGene.update(paml7v8)
@@ -139,12 +140,12 @@
resLine = "\t".join(lBaseRes + list(dGene.values()))
allRes.append(resLine)

bppLlhRes = [str(bppLlh[k]) for k in ["M1","M2","M7","M8"]]
bppLlhRes = [str(bppLlh[k]) for k in ["M1","M2","M7","M8","DFP07_0","DFP07"]]
llh.write(baseName+"\tBPP\t"+"\t".join(bppLlhRes)+"\n")

if type(bppLlh) is dict:
pamlLlhRes = [str(value) for value in pamlLlh.values()]
llh.write(baseName+"\tPAML\t"+"\t".join(pamlLlhRes)+"\n")
llh.write(baseName+"\tPAML\t"+"\t".join(pamlLlhRes)+2*"\tna"+"\n")
else:
llh.write(baseName+"\tPAML\tna\n")

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