add test-op dir

Author: nservant

test-op/config_test_latest.txt

@@ -0,0 +1,91 @@
+# Please change the variable settings below if necessary
+
+#########################################################################
+## Paths and Settings  - Do not edit !
+#########################################################################
+
+TMP_DIR = tmp
+LOGS_DIR = logs
+BOWTIE2_OUTPUT_DIR = bowtie_results
+MAPC_OUTPUT = hic_results
+RAW_DIR = rawdata
+
+#######################################################################
+## SYSTEM - PBS - Start Editing Here !!
+#######################################################################
+N_CPU = 4
+LOGFILE = hicpro.log
+
+JOB_NAME = IMR90_split
+JOB_MEM = 10gb
+JOB_WALLTIME = 6:00:00
+JOB_QUEUE = batch
+JOB_MAIL = [email protected]
+
+#########################################################################
+## Data
+#########################################################################
+
+PAIR1_EXT = _R1
+PAIR2_EXT = _R2
+
+#######################################################################
+## Alignment options
+#######################################################################
+
+FORMAT = phred33
+MIN_MAPQ = 0
+
+BOWTIE2_IDX_PATH = /home/nservant/Bureau/hicpro_dev/test-op/bowtie2_indexes/
+BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
+BOWTIE2_LOCAL_OPTIONS =  --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder
+
+#######################################################################
+## Annotation files
+#######################################################################
+
+REFERENCE_GENOME = hg19
+GENOME_SIZE = chrom_hg19.sizes
+
+#######################################################################
+## Allele specific
+#######################################################################
+
+ALLELE_SPECIFIC_SNP = 
+
+#######################################################################
+## Digestion Hi-C
+#######################################################################
+
+GENOME_FRAGMENT = HindIII_resfrag_hg19.bed
+LIGATION_SITE = AAGCTAGCTT
+MIN_FRAG_SIZE = 100
+MAX_FRAG_SIZE = 100000
+MIN_INSERT_SIZE = 100
+MAX_INSERT_SIZE = 600
+
+#######################################################################
+## Hi-C processing
+#######################################################################
+
+MIN_CIS_DIST =
+GET_ALL_INTERACTION_CLASSES = 1
+GET_PROCESS_SAM = 1
+RM_SINGLETON = 1
+RM_MULTI = 1
+RM_DUP = 1
+
+#######################################################################
+## Contact Maps
+#######################################################################
+
+BIN_SIZE = 500000 1000000
+MATRIX_FORMAT = upper
+
+#######################################################################
+## ICE Normalization
+#######################################################################
+MAX_ITER = 100
+FILTER_LOW_COUNT_PERC = 0.02
+FILTER_HIGH_COUNT_PERC = 0
+EPS = 0.1

test-op/run-test-op.sh

@@ -0,0 +1,82 @@
+#!/bin/bash
+
+function die
+{
+    echo -e "Unit testing failed !"
+    exit 1
+}
+
+## HiC-Pro should be install and in the PATH
+which HiC-Pro > /dev/null;
+if [ $? != "0" ]; then
+    echo -e "Can not proceed without HiC-Pro, please install and/or set the PATH variable"
+    exit 1;
+fi
+
+## Get data
+if [[ $(ls bowtie2_indexes | wc -l) == 0 ]]; then
+    echo -e "bowtie2_indexes folder looks empty. Please provide the hg19 bowtie2 indexes or download them using "
+    echo -e "wget ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/hg19.zip"
+    exit 1
+fi
+
+#wget https://zerkalo.curie.fr/partage/HiC-Pro/HiCPro_testdata.tar.gz && tar -zxvf HiCPro_testdata.tar.gz
+#/bin/rm -f HiCPro_testdata.tar.gz
+
+RES_PREFIX=HiC_Pro_test-op
+CONFIG=config_test_latest.txt
+RUN_CLUSTER_MODE=0
+
+## standalone complete pipeline
+
+cmd="time HiC-Pro -i test_data/ -o ${RES_PREFIX} -c ${CONFIG}"
+echo $cmd
+eval $cmd
+if [[ $? != 0 ]]; then die; fi
+
+## standalone stepwise pipeline
+
+cmd="time HiC-Pro -i test_data -o ${RES_PREFIX}_stepwise1 -c ${CONFIG} -s mapping -s quality_checks"
+echo $cmd
+eval $cmd
+if [[ $? != 0 ]]; then die; fi
+
+cmd="time HiC-Pro -i ${RES_PREFIX}_stepwise1/bowtie_results/bwt2 -o ${RES_PREFIX}_stepwise2 -c ${CONFIG} -s proc_hic -s quality_checks"
+echo $cmd
+eval $cmd
+if [[ $? != 0 ]]; then die; fi
+
+cmd="time HiC-Pro -i ${RES_PREFIX}_stepwise2/hic_results/data/ -o ${RES_PREFIX}_stepwise3 -c ${CONFIG} -s merge_persample -s build_contact_maps -s ice_norm"
+echo $cmd
+eval $cmd
+if [[ $? != 0 ]]; then die; fi
+
+cmd="time HiC-Pro -i ${RES_PREFIX}_stepwise3/hic_results/data/ -o ${RES_PREFIX}_stepwise4 -c ${CONFIG} -s build_contact_maps"
+echo $cmd
+eval $cmd
+if [[ $? != 0 ]]; then die; fi
+
+cmd="time HiC-Pro -i  ${RES_PREFIX}_stepwise4/hic_results/matrix/ -o ${RES_PREFIX}_stepwise5 -c ${CONFIG} -s ice_norm"
+echo $cmd
+eval $cmd
+if [[ $? != 0 ]]; then die; fi
+
+## Cluster complete pipeline
+if [[ $RUN_CLUSTER_MODE == 1 ]]; then
+    time HiC-Pro -i test_data/ -o ${RES_PREFIX}_cluster -c ${CONFIG} -p
+    file2sub=$(find ${RES_PREFIX}_cluster -name "*step1*")
+    qsub ${file2sub}
+fi
+
+## as test
+#export CONFIG=config_test_as.txt
+
+#time HiC-Pro -i test_data_as -o ${RES_PREFIX}_5 -c config_test_as.txt
+
+## dnase test
+#export CONFIG=config_test_dnase.txt
+
+#time HiC-Pro -i test_data/ -o ${RES_PREFIX}_6 -c config_test_dnase.txt
+
+
+#/bin/rm -rf HiC_Pro_test-op*