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parsing signalp results: handle SP v6 where there is no actual CS reported (rare but seems to happen)
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Lines changed: 7 additions & 6 deletions

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funannotate/library.py

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -7400,12 +7400,13 @@ def parsePhobiusSignalP(phobius, sigP, membrane_annot, secretome_annot):
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if "\t" in line:
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cols = line.split("\t")
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if cols[1] != "OTHER": # then signal peptide
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ID, prediction, score1, score2, position = cols[:5]
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ID = ID.split(" ")[0]
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components = position.split()
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pos = components[2].split("-")[0]
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prob = components[-1]
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sigpDict[ID] = [pos, "", prob]
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if len(cols) >= 5:
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ID, prediction, score1, score2, position = cols[:5]
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ID = ID.split(" ")[0]
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components = position.split()
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pos = components[2].split("-")[0]
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prob = components[-1]
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sigpDict[ID] = [pos, "", prob]
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else:
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sigpDict = pSecDict
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# write annotation files

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