From 1227280755ad0c472cf7196a873140b396e9c289 Mon Sep 17 00:00:00 2001 From: Guoyi Zhang Date: Thu, 19 Sep 2024 13:48:13 +1000 Subject: [PATCH] fix: skip genes --- RGBEPP.d | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/RGBEPP.d b/RGBEPP.d index 454ea60..3b883c5 100644 --- a/RGBEPP.d +++ b/RGBEPP.d @@ -473,9 +473,12 @@ void processTrimming(string[] ARG_G, string DirAlign, string DirTrim, string Pat string inputFastaAA = DirAA_out ~ "/" ~ gene ~ ".fasta"; string inputBackTransNT = DirNT_out ~ "/" ~ gene ~ ".fasta"; string outputFastaNT = DirTrimNT ~ "/" ~ gene ~ ".fasta"; - - string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-automated1"]; - executeCommand(cmdTrim); + if (exists(inputFastaAA) && exists(inputBackTransNT)) { + string[] cmdTrim = [PathTrimal, "-in", inputFastaAA, "-backtrans", inputBackTransNT, "-out", outputFastaNT, "-automated1"]; + executeCommand(cmdTrim); + } else { + writeln("Skipping gene: ", gene, " as files are missing."); + } } writeln("Trimming::End");