Add new anaysis

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)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+#numcer.tab <- args[1]
+nucmer.tab <- "/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/CPM_analysis/IMP.processed.coords.filtered"
+
+nucmer.dat <- read.table(nucmer.tab, sep="\t", header=T)
+colnames(nucmer.dat) <- c("rstart", "rend", "cstart", "cend", "rlen", "clen", "pident", "tags")
+

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')

additional_analyses/README

@@ -8,4 +8,5 @@ This folder contains 8 directories:
 6. comparison: Comparing assemblies single vs multi-omic, IMP vs MetAMOS
 7. HMP_gene_catalog: Mapping data to HMP gene catalog (incomplete)
 8. MT_genomes: Analysis of genomes assembled only from MT data
+9. CPM_measure_analysis: This relates to the analysis based on the composite measure used by Deng et.al, (2015)