From 80dd8da11087a0965c63104dd6a58d140f6fa2fc Mon Sep 17 00:00:00 2001
From: Migun Shakya <microbeatic@gmail.com>
Date: Fri, 26 Oct 2018 11:57:39 -0600
Subject: [PATCH] trying setup py for installations

---
 scripts/gage_analysis.R | 21 +++++++++++++++++----
 setup.py                |  3 ++-
 2 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/scripts/gage_analysis.R b/scripts/gage_analysis.R
index e49a234..97f5721 100644
--- a/scripts/gage_analysis.R
+++ b/scripts/gage_analysis.R
@@ -8,6 +8,8 @@ option_list <- list(
               help = "directory containing results of EdgeR or DESeq2"),
   make_option(c("-m", "--method"), action = "store",
               help = "output of which results to conduct gage analysis on"),
+  make_option(c("-c", "--org_code"), action = "store",
+              help = "kegg orgainsm code to download pathway information"),
   make_option(c("-o", "--out_dir"), action = "store",
               help = "output directory")
 )
@@ -17,6 +19,7 @@ opt <- parse_args(OptionParser(option_list = option_list))
 #
 dir <- opt$dir
 method <- opt$method
+code <- opt$org_code
 
 #==============================================================================#
 # create the output directory
@@ -25,12 +28,22 @@ method <- opt$method
 
 # grab fold change files
 if ( method == "edgeR"){
-    temp = list.files(path=dir, pattern="gene_*_et.csv")
+    fcs = list.files(path = dir, pattern = "gene_*_et.csv", full.names = TRUE)
 
 } else if (method == "DESeq2")
 {   
-    temp = list.files(pattern="gene_*_et.csv")
-    print(temp)
+    fcs = list.files(path = dir, pattern = "gene_*_et.csv", full.names = TRUE)
+    
+}
+
+
+# perform gage analysis, one fc at a time
+
+for (fc in fcs){
+    fc_df <- read.csv(fc, row.names = 1)
+    print(head(fc_df))
 
 }
-# read in all the 
\ No newline at end of file
+
+
+gene_sets <- kegg.gsets(species = code)
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 000b85f..6657052 100644
--- a/setup.py
+++ b/setup.py
@@ -8,9 +8,10 @@
     description="RNAseq pipeline",
     author="Migun Shakya",
     author_email="migun@lanl.gov",
-    url="https://github.com/mshakya/pypiret",
+    url="https://github.com/mshakya/piret",
     install_requires=open("requirements.txt").read().splitlines(),
     packages=find_packages(),
+    scripts=['bin/piret'],
     license="Apache License 2.0",
     platforms="Posix; MacOS X",
     classifiers=[