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#! /usr/bin/perl
# This script maps oligonucleotides. (i.e.) restriction site,
# which are normally to short to be mapped by conventional 
# methods.

# NOTE, incomplete have to add palindrome
# subroutine

use strict; use warnings;
use Getopt::Long;

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library(DESeq2)
library(arrayQualityMetrics)
library(gplots)
library(RColorBrewer)
library(biomaRt)
library(ReportingTools)
library(org.Mm.eg.db)
library(plyr)
library(pathview)
setwd("C:/Users/Yaroslav/Dropbox/Jacobs_project/")

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library(DEXSeq)
library(pasilla)

setwd("/path/to/dir")

# Doing the vignette
# Get locations for count files and flattened annotation file in gff formar
inDir = "~/Dropbox/Jacobs_project/relative_exon_usage/exon_counts"
countFiles = list.files(inDir, pattern="exon.txt$", full.names=TRUE)
countFiles

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# Go through vignette
library(DiffBind)
library(ChIPpeakAnno)
library(org.Mm.eg.db)
library(KEGG.db)
library(reactome.db)
setwd("~/Projects/grey_miseq/diffbind_analysis/")

# Analyze real samples
setwd("~/Projects/grey_miseq/diffbind_analysis/")

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library("topGO")
library("ChIPpeakAnno")
library("org.Mm.eg.db")
library("plyr")

## Get universe ids
x <- org.Mm.egGO
mapped_genes <- mappedkeys(x)
universeIDs <- unique(mapped_genes)

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#! /usr/bin/perl
# Grab lines between 2 matches and print them out
# In this case I'm using it to print out read length 
# distribution from FastQC's fastqc_data.txt

my $dir = shift; # take directory name
	
open ( my $reads_file, "<", "$dir/fastqc_data.txt" ) or die "Cannot open original reads file: $!\n";

# Extract number of reads 

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library(edgeR)
library(reshape2)
library(plyr)

# Get library distribution profile 
setwd("~/Projects/Champion_smallRNA/length_distr/")
list.files()

d <- readDGE(list.files(), columns = c(1,2))
counts <- d$count

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heatmap.2(as.matrix(res), scale = "row", col = redgreen(75), 
            ColSideColors=color_vector, trace = "none",
            margins = c(14, 13), cexRow = 0.7)

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###########################################################################
## Exploratory analysis
library(edgeR)
library(DESeq2)
library(arrayQualityMetrics)
library(gplots)
library(RColorBrewer)
library(ggplot2)

setwd("~/Projects/Champion_smallRNA/comparisons")

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library(gage)
library(pathview)
library("gageData")
library(biomaRt)

# read variance stabilized expression data
vsd <- read.table("expression_data/expressions_vsd.txt", header = T, row.names = 1)

# Rename samples using descriptive sample names
coldata <- read.table("sample_layout.txt", sep="\t", header=T, row.names=1)