remove unneeded files and example tsv

README.md

 # example-snakemake
 
-example snakemake workflow for workflow repository
\ No newline at end of file
+example snakemake workflow for workflow repository
+
+~input.tsv~ may look like
+
+```
+sample	reference	fwd_pair	rev_pair
+DRR198805_c1e4	ecoli.fasta	DRR198805_c1e4_R1_001.fastq.gz	DRR198805_c1e4_R2_001.fastq.gz
+DRR198805_c1e4.2	ecoli.fasta	DRR198805_c1e4.2_R1_001.fastq.gz	DRR198805_c1e4.2_R2_001.fastq.gz
+DRR198805_c2e4	ecoli.fasta	DRR198805_c2e4_R1_001.fastq.gz	DRR198805_c2e4_R2_001.fastq.gz
+ERR4147226_c1e4	ecoli.fasta	ERR4147226_c1e4_R1_001.fastq.gz ERR4147226_c1e4_R2_001.fastq.gz
+ERR4147226_c1e4.2	ecoli.fasta	ERR4147226_c1e4.2_R1_001.fastq.gz ERR4147226_c1e4.2_R2_001.fastq.gz
+ERR4147226_c1e4.3	ecoli.fasta	ERR4147226_c1e4.3_R1_001.fastq.gz ERR4147226_c1e4.3_R2_001.fastq.gz
+ERR4147226_c1e4.4	ecoli.fasta	ERR4147226_c1e4.4_R1_001.fastq.gz ERR4147226_c1e4.4_R2_001.fastq.gz
+ERR4147226_c2e4	ecoli.fasta	ERR4147226_c2e4_R1_001.fastq.gz ERR4147226_c2e4_R2_001.fastq.gz
+ERR4147226_c2e4.2	ecoli.fasta	ERR4147226_c2e4.2_R1_001.fastq.gz ERR4147226_c2e4.2_R2_001.fastq.gz
+```

design.tsv

-sample	reference	fwd_pair	rev_pair
-DRR198805_c1e4	ecoli.fasta	DRR198805_c1e4_R1_001.fastq.gz	DRR198805_c1e4_R2_001.fastq.gz

scripts/binning_fasta_as_bed.sh

-#!/bin/bash
-
-REF_FAI=$1
-BINNED_REF=$2
-BIN_SIZE=${3:-100000}
-
-
-	#for (binStart = start; binStart < (stop - binSize); binStart += binSize) {
-awk -v "BS=${BIN_SIZE}" '
-BEGIN {
-	binSize = BS;
-	binIdx = 0;
-}
-{
-	chr = $1;
-	start = 0;
-	stop = $2;
-	for (binStart = start; binStart <= stop; binStart += binSize) {
-		print chr"\t"binStart"\t"(binStart + binSize)"\tbin-"binIdx;
-		binIdx++;
-	}
-}
-' ${REF_FAI} > ${BINNED_REF}
-
-
-
-
-

scripts/plotMutations.Rscript

-#!/usr/bin/env Rscript
-
-suppressPackageStartupMessages(require(optparse))
-suppressPackageStartupMessages(require(ggplot2))
-suppressPackageStartupMessages(require(viridis))
-
-option_list = list(
-	make_option(c("-i", "--input"), action="store", default=NA, type='character', help="input filename"),
-	make_option(c("-g", "--genome"), action="store", default=NA, type='character', help="genome name to display in title"),
-	make_option(c("-b", "--binsize"), action="store", default=NA, type='character', help="size of bins, with unit (eg. 50 kb)"),
-	make_option(c("-o", "--output"), action="store", default=NA, type='character', help="output filename")
-)
-opt = parse_args(OptionParser(option_list=option_list))
-
-#d <- read.table(opt$input, header=F, stringsAsFactor=T, col.names=c("chr", "start", "stop", "id", "mutations", "ref_base", "read_base", "check", "info"))
-d <- read.table(opt$input, header=F, stringsAsFactor=T, col.names=c("chr", "position", "stop", "id", "mutations"))
-#d$chr <- factor(d$chr, levels = c('YLS.canu_hybrid_1', 'YLS.canu_hybrid_2', 'YLS.canu_hybrid_3', 'YLS.canu_hybrid_4', 'YLS.canu_hybrid_5', 'YLS.canu_hybrid_6', 'YLS.canu_hybrid_7', 'YLS.canu_hybrid_8'))
-#d$chr <- factor(d$chr, levels = c('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY'))
-
-d <- with(d, d[order(chr),])
-
-if (!require(ggplot2)) install.packages('ggplot2')
-library(ggplot2)
-cnt_chr = length(unique(d$chr))
-max_pos_chr = aggregate(stop ~ chr, data=d, max)
-pdf(opt$output, width=7,height=1+0.2*cnt_chr)
-
-p <- ggplot(data=d, aes(x=position, y=1)) +
-	facet_grid(chr ~ ., switch='y') +
-	geom_tile(aes(fill=mutations)) +
-	ggtitle(paste("SNPs in ", opt$genome, ", binsize=", opt$binsize, sep="")) +
-	#geom_rect(data=d, mapping=aes(xmin=x1, xmax=x2, ymin=y1, ymax=y2, fill=t), color="black", alpha=0.5) +
-	#geom_rect(data=d, mapping=aes(xmin=0, xmax=max_pos_chr[chr], ymin=0, ymax=1, fill=t), color="black", alpha=0.5) +
-	theme(
-		axis.title.y=element_blank(), #text("contig"),
-		axis.text.y=element_blank(),
-		axis.ticks.y=element_blank(),
-		strip.text.y = element_text(angle = 180)) +
-	theme(
-		panel.grid.major = element_blank(),
-		panel.grid.minor = element_blank(),
-		panel.background = element_blank()
-		#panel.border = element_rect(colour = "black", fill=NA, size=0.1)
-	) +
-	#scale_fill_gradient(low="white", high="black", breaks=seq(min(d$mutations),max(d$mutations),(max(d$mutations)-min(d$mutations))/4))
-	#scale_fill_gradientn(colors = c('darkorange1', 'darkmagenta', 'navyblue'), breaks=seq(min(d$mutations),max(d$mutations),(max(d$mutations)-min(d$mutations))/4))
-	scale_fill_viridis(direction=-1,breaks=seq(min(d$mutations),max(d$mutations),(max(d$mutations)-min(d$mutations))/4))
-	#scale_fill_gradientn(colors = c('darkorange1', 'darkmagenta', 'navyblue'), breaks=seq(0, 500, 125))
-	#scale_fill_gradientn(colours = rainbow(5), breaks=seq(min(d$mutations),max(d$mutations),(max(d$mutations)-min(d$mutations))/4))
-	#scale_colour_grey(breaks=seq(min(d$mutations),max(d$mutations),(max(d$mutations)-min(d$mutations))/4))
-
-print(p)
-dev.off()
-