add a case_study file, which is easy to understand

case_study.sh

@@ -0,0 +1,121 @@
+#!/bin/bash
+
+# processing the input parameter
+while [[ -n $1 ]]; do
+        # echo "\$1=$1"
+        case $1 in
+                -f | --filename )       shift
+                                                FULLFILE=$1
+                                                ;;                      
+        esac
+        shift
+done
+FILE_N=$(basename "$FULLFILE")
+EXTENSION="${FILE_N##*.}"
+# use the filename to name the tmp files
+FILENAME="${FILE_N%.*}"
+
+NUM=$(fgrep -o '>' $FULLFILE | wc -l)
+PREFIX="signal"
+
+# the input should be a fasta file
+# we should make a tmp directory named after the input file to
+# store the tmp files
+mkdir -p $FILENAME
+
+source activate tensorflow_cdpm
+# preprocessing, sampling the read
+# satisfy the converage and length distritubtion requirement
+echo "Executing the preprocessing step..."
+
+python2 ./util/genome_preprocess.py \
+	-i $FULLFILE \
+	-o $FILENAME/processed_genome \
+	-r 1
+
+python2 ./util/genome_sampling.py \
+	-i $FILENAME/processed_genome \
+	-p $FILENAME/sampled_read \
+	-n 100 \
+	-K 0 \
+	-l 8000 \
+	-d 3 \
+	-S 0 
+
+# pore model translation
+# convert the signal to the original range
+# signal duplication 
+# done within pore model
+echo "Finished the preprocessing step!"
+echo "Running the context-dependent pore model..."
+rm -rf $FILENAME/signal/*
+mkdir -p ./signal
+rm -rf $FILENAME/align/*
+mkdir -p $FILENAME/align
+rm -rf $FILENAME/fast5/*
+mkdir -p $FILENAME/fast5
+
+curdir="$(pwd)"
+
+export DeepSimulatorHome=$curdir
+python2 ./pore_model/src/context_simulator.py \
+	-i $FILENAME/sampled_read.fasta \
+	-p $FILENAME/signal/signal \
+	-l $FILENAME/align/align \
+	-t 32 \
+	-f 950 -s 1.0 \
+	-S 0 \
+	-u 1 \
+	-F $FILENAME/fast5 \
+	-T ./util/template.fast5
+
+
+# change the signal file to fasta5 file
+# echo "Finished generate the simulated signals!"
+# echo "Converting the signal into FAST5 files..."
+# rm -rf ./fast5/*
+# mkdir -p ./fast5
+# signal_dir="./signal/"
+# python2 ./signal_to_fast5/fast5_modify_signal.py \
+# 	-i ./signal_to_fast5/template.fast5 \
+# 	-s ${signal_dir} \
+# 	-d ./fast5 
+
+# basecalling using albacore
+
+echo "Finished format converting!"
+echo "Running Albacore..."
+source activate basecall
+FAST5_DIR="$FILENAME/fast5"
+FASTQ_DIR="$FILENAME/fastq"
+rm -rf $FASTQ_DIR/*
+mkdir -p $FASTQ_DIR
+read_fast5_basecaller.py -i $FAST5_DIR -s $FASTQ_DIR \
+	-c r94_450bps_linear.cfg -o fastq -t 56
+
+source activate tensorflow_cdpm
+
+# check result
+echo "Basecalling finished!"
+echo "Checking the read accuracy..."
+
+
+cat $FILENAME/fastq/workspace/pass/*.fastq > $FILENAME/pass.fastq 2>$FILENAME/err
+cat $FILENAME/fastq/workspace/fail/*.fastq > $FILENAME/fail.fastq 2>$FILENAME/err
+
+pass_num=`grep "^@" $FILENAME/pass.fastq | wc | awk '{print $1}'`
+fail_num=`grep "^@" $FILENAME/fail.fastq | wc | awk '{print $1}'`
+cat $FILENAME/pass.fastq $FILENAME/fail.fastq > $FILENAME/test.fastq
+./util/minimap2 -Hk19 -t 32 -c $FULLFILE \
+	$FILENAME/test.fastq 1> $FILENAME/mapping.paf 2> $FILENAME/err
+rm -f $FILENAME/err
+accuracy=`awk 'BEGIN{a=0;b=0}{a+=$10/$11;b++}END{print a/b}' $FILENAME/mapping.paf`
+totalnum=`grep "^@" $FILENAME/test.fastq | wc | awk '{print $1}'`
+echo "Here is the mapping identity: $accuracy of $totalnum (pass $pass_num + fail $fail_num) reads passed base-calling."
+echo "$accuracy $totalnum $pass_num $fail_num" > $FILENAME/accuracy
+# remove temporary files
+rm -rf $FILENAME/fastq
+rm -f $FILENAME/test.fastq
+
+#---------- exit -----------#
+exit 0