Remove CPM measure scripts

additional_analyses/CPM_measure_analysis/rules/find_AL.rule

-rule find_AL:
-    input:
-           "{assm}.processed.coords.filtered"
-    output:
-           "{assm}.processed.coords.filtered_AL"
-    shell:
-           """
-           Rscript
-           """

additional_analyses/CPM_measure_analysis/rules/find_AL1000.rule

-rule find_AL1000:
-input:
-       "{assm}.processed.coords.filtered"
-output:
-       "{assm}.processed.coords.filtered_AL1000"
-shell:
-       """
-       Rscript
-       """

additional_analyses/CPM_measure_analysis/rules/find_C1000.rule

-rule find_C1000:
-input:
-       "{assm}.processed.coords.filtered_AL1000"
-output:
-       "{assm}.processed.coords.filtered_C1000"
-shell:
-       """
-       bedtools merge {input} > output
-       """

additional_analyses/CPM_measure_analysis/rules/process_nucmer.rule

-rule process_table:
-    input:
-       "%s/{assm}.coords.filtered" % NUCMER_RES
-    output:
-       "{assm}.processed.coords.filtered"
-    shell:
-        """
-        sed -e "s/ | /\t/g" {input} | grep -v "^==========" > {output}
-        """

additional_analyses/CPM_measure_analysis/src/getAL_info.R

-#!/bin/R
-require(stringr)
-require(bedr)
-
-args <- commandArgs(trailingOnly = TRUE)
-
-#numcer.tab <- args[1]
-
-## Read in nucmer table
-nucmer.tab <- "/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/metaquast_output/CPM_analysis/IMP.processed.coords.filtered"
-nucmer.dat <- read.delim(nucmer.tab, sep="\t", header=F)
-colnames(nucmer.dat) <- c("rstart", "rend", "cstart", "cend", "rlen", "clen", "pident", "ref", "contig", "ambiguity")
-
-al <- nucmer.dat 
-al1000 <-  subset(nucmer.dat, clen >= 1000)
-bed <- nucmer.dat[, c("contig", "cstart", "cend")]
-bed.1 <-  subset(bed, cstart < cend)
-
-# Calculate M: sum length of all aligned regions
-M <- sum(al$clen)
-
-# Calculate N: sum length of all unaligned regions
-macr <-  
-    max(al$clen) 
-
-## Write out AL file
-write.table(al, 
-	    "/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/metaquast_output/CPM_analysis/IMP.processed.coords.filtered_AL", 
-	    row.names=F, 
-	    col.names=F, 
-	    sep="\t", 
-	    quote=F)
-
-## Write out AL file
-write.table(subset(nucmer.dat, clen >= 1000), 
-	    "/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/metaquast_output/CPM_analysis/IMP.processed.coords.filtered_AL1000", 
-	    row.names=F, 
-	    col.names=F, 
-	    sep="\t", 
-	    quote=F)
-
-## Write out bedfile
-write.table(bed, 
-	    "/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/metaquast_output/CPM_analysis/IMP.processed.coords.filtered.bed", 
-	    row.names=F, 
-	    col.names=F, 
-	    sep="\t", 
-	    quote=F)
-
-bed.2 <- unique(paste(bed$contig, ":",  bed$cstart, "-", bed$cend, sep=""))
-bed2index(bed)
-
-bed.3 <- bed.2[is.valid.region(bed.2, check.chr=F)]
-
-convert2bed(bed.2, check.zero.based=F, check.valid=F)
-
-bedr.merge.region(bed.3, check.chr=F, check.valid=T, check.sort=T, check.zero.based=T)

additional_analyses/CPM_measure_analysis/src/preload_modules.sh

-IMP_ENV=/mnt/nfs/projects/ecosystem_biology/local_tools/IMP/dependencies
-
-export PATH=$IMP_ENV/fastuniq/source:$PATH
-export PATH=$IMP_ENV/sortmerna-2.0:$PATH
-export PATH=$IMP_ENV/sortmerna-2.0/scripts:$PATH
-export PATH=$IMP_ENV/bwa-0.7.9a:$PATH
-export PATH=$IMP_ENV/idba-1.1.1/bin:$PATH
-export PATH=$IMP_ENV/megahit:$PATH
-export PATH=$IMP_ENV/CAP3:$PATH
-export PATH=$IMP_ENV/prokka/bin:$PATH
-export PATH=$IMP_ENV/quast:$PATH
-export PATH=$IMP_ENV/quast/libs/genemark/linux_64:$PATH
-export PATH=$IMP_ENV/prokka/binaries/linux:$PATH
-export PATH=$IMP_ENV/cd-hit-v4.6.1-2012-08-27_OpenMP:$PATH
-
-# Samtools must be full path!
-export PATH=/mnt/nfs/projects/ecosystem_biology/local_tools/IMP/dependencies/samtools-0.1.19:$PATH
-export PATH=/mnt/nfs/projects/ecosystem_biology/local_tools/IMP/dependencies/bedtools2/bin:$PATH
-export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/IMP/dependencies/bedtools2/bin
-export PATH=$PATH:$IMP_ENV/bedtools2/bin
-export PATH=/mnt/nfs/projects/ecosystem_biology/local_tools/IMP/dependencies/quast:$IMP_ENV:$PATH
-
-#source this file before execution of snakefile
-#module load Python
-source /mnt/nfs/projects/ecosystem_biology/local_tools/IMP/bin/activate
-module load lang/Java/1.7.0_21
-
-#
-#module load MEGAHIT
-#module load BWA 
-#module load SAMtools 
-#module load BEDTools
-#module load OpenBLAS 
-#module load Boost/1.53.0-ictce-5.3.0 
-#
-#export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/idba-1.1.1.icc/bin
-#
-#module load CAP3
-#
-##symbolic links for prokka db 
-#module load prokka
-#
-#export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/tabix-0.2.6
-#export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/gkno_launcher/tools/freebayes/bin
-#export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/vcftools/bin
-#export PERL5LIB=$PERL5LIB:/mnt/nfs/projects/ecosystem_biology/local_tools/vcftools/perl
-#export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/Platypus/Platypus_0.7.9.1
-#
-#module load R
-#Rscript -e "install.packages('beanplot')"
-#
-#module list
-
-#The Boost C++ Libraries were successfully built!
-#
-#The following directory should be added to compiler include paths:
-#
-#    /mnt/src_nfs1/projects/ecosystem_biology/local_tools/IMP/dependencies/boost_1_54_0
-#
-#The following directory should be added to linker library paths:
-#
-#    /mnt/src_nfs1/projects/ecosystem_biology/local_tools/IMP/dependencies/boost_1_54_0/stage/lib
-#

additional_analyses/CPM_measure_analysis/workflow/cpm_workflow

-import subprocess
-
-#TMPDIR = os.environ.get("TMPDIR", "/tmp")
-#SRCDIR = os.environ.get("SRCDIR", "src")
-#CONFIG = os.environ.get("CONFIG", "config_normalNode.json")
-#DBPATH = os.environ.get("DBPATH", "/mnt/nfs/projects/ecosystem_biology/local_tools/IMP/dependencies/prokka/db")
-#
-#configfile: CONFIG
-#
-#MEMCORE = os.environ.get("MEMCORE", config['memory_per_core_gb'])
-#THREADS = os.environ.get("THREADS", config['threads'])
-#MEMTOTAL = os.environ.get("MEMTOTAL", config['memory_total_gb'])
-
-## Define input directories
-# Nucmer results (from metaQUAST)
-NUCMER_RES = "/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/SM/combined_reference/contigs_reports/nucmer_output"
-
-# metaQUAST table results
-MQ_RES = "/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/SM/combined_reference/contigs_reports/nucmer_output"
-
-
-## Define samples
-ASSMS = [ 'IMP', 'IMP-megahit', 'IMP_MG', 'IMP_MT', 'MetAmos_MG', 'MetAmos_MGMT', 'MOCAT_MG', 'MOCAT_MGMT' ]
-
-## Define output directory
-OUTDIR = os.environ.get("OUTDIR", "/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/CPM_analysis")
-
-workdir:
-    OUTDIR
-
-include:
-    '../rules/process_nucmer.rule'
-
-#include:
-#    '../rules/find_AL.rule'
-#
-rule CPM_ALL:
-    input:
-       expand("{assm}.processed.coords.filtered", assm=ASSMS),
-       #expand("{assm}.processed.coords.filtered_AL", assm=ASSMS)
-    output:
-       touch('cpm.done')