From e93f03f204b9e4f6a5d24a0c2cc9cb64f774ac8b Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Tue, 9 May 2017 09:28:07 -0500
Subject: [PATCH] fix chipseeker mm10
---
workflow/scripts/runChipseeker.R | 4 ++--
workflow/scripts/runMemechip.py | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/workflow/scripts/runChipseeker.R b/workflow/scripts/runChipseeker.R
index e238a4a..b20df78 100644
--- a/workflow/scripts/runChipseeker.R
+++ b/workflow/scripts/runChipseeker.R
@@ -18,8 +18,8 @@ txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
}
if(genome=="GRCm38")
{
-library(TxDb.Hsapiens.UCSC.mm10.knownGene)
-txdb <- TxDb.Hsapiens.UCSC.mm10.knownGene
+library(TxDb.Mmusculus.UCSC.mm10.knownGene)
+txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
}
if(genome=="GRCh38")
{
diff --git a/workflow/scripts/runMemechip.py b/workflow/scripts/runMemechip.py
index 36f84c5..b1f848f 100644
--- a/workflow/scripts/runMemechip.py
+++ b/workflow/scripts/runMemechip.py
@@ -29,7 +29,7 @@ def prepare_argparser():
argparser.add_argument("-l","--limit",dest = "limit",type=int,default=-1, help="Top limit of peaks")
return(argparser)
-def rc():
+def rc(seq):
comps = {'A':"T",'C':"G",'G':"C",'T':"A","N":"N"}
return ''.join([comps[x] for x in seq.upper()[::-1]])
--
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