ngs_INIT.sh

#!/bin/bash

# Copyright (c) 2012,2013, Stephen Fisher and Junhyong Kim, University of
# Pennsylvania.  All Rights Reserved.
#
# You may not use this file except in compliance with the Kim Lab License
# located at
#
#     http://kim.bio.upenn.edu/software/LICENSE
#
# Unless required by applicable law or agreed to in writing, this
# software is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
# CONDITIONS OF ANY KIND, either express or implied.  See the License
# for the specific language governing permissions and limitations
# under the License.

##########################################################################################
# SINGLE-END READS:
# INPUT: $RAW/$SAMPLE/*_R1_*.gz
# OUTPUT: $SAMPLE/raw/unaligned_1.fq
#
# PAIRED-END READS:
# INPUT: $RAW/$SAMPLE/*_R1_*.gz and $RAW/$SAMPLE/*_R2_*.gz
# OUTPUT: $SAMPLE/raw/unaligned_1.fq and $SAMPLE/raw/unaligned_2.fq
##########################################################################################

##########################################################################################
# USAGE
##########################################################################################

NGS_USAGE+="Usage: `basename $0` init OPTIONS sampleID    --  prepare read file(s) for processing\n"

##########################################################################################
# HELP TEXT
##########################################################################################

ngsHelp_INIT() {
	echo -e "Usage:\n\t`basename $0` init [-i inputDir] [-se] sampleID"
	echo -e "Input:\n\tinputDir/sampleID/*_R1_*.gz\n\tinputDir/sampleID/*_R2_*.gz (paired-end reads)"
	echo -e "Output:\n\tsampleID/init/unaligned_1.fq\n\tsampleID/init/unaligned_2.fq (paired-end reads)"
	echo -e "Options:"
	echo -e "\t-i - parent directory containing subdirectory with compressed fastq files (default: ./raw). This is the parent directory of the sample-specific directory. The sampleID will be used to complete the directory path (ie inputDir/sampleID)."
	echo -e "\t-se - single-end reads (default: paired-end)\n"
	echo -e "By default this expects the directory './raw/sampleID' that contains the demultiplexed reads. The demultiplexed reads need to be gzipped. The files containing the first reads need to include '_R1_' in their filenames and the second read files need to contain '_R2_' in the filenames. If inputDir is used then the read files are expected to reside in 'inputDir/sampleID'. \n"
	echo -e "This will uncompress the raw files and place them in the directory './sampleID/init'. Output files are named 'unaligned_1.fq' (first reads) and 'unaligned_2.fq' (second reads). Only unaligned_1.fq will be generated in the case of single-end reads."
}

##########################################################################################
# LOCAL VARIABLES WITH DEFAULT VALUES. Using the naming convention to
# make sure these variables don't collide with the other modules.
##########################################################################################

ngsLocal_INIT_INP_DIR=$RAW

##########################################################################################
# PROCESSING COMMAND LINE ARGUMENTS
# INIT args: -se (optional), sampleID
##########################################################################################

ngsArgs_INIT() {
	if [ $# -lt 1 ]; then printHelp "INIT"; fi
	
	# getopts doesn't allow for optional arguments so handle them manually
	while true; do
		case $1 in
			-i) ngsLocal_INIT_INP_DIR=$2
				shift; shift;
				;;
			-se) SE=true
				shift;
				;;
			-*) printf "Illegal option: '%s'\n" "$1"
				printHelp $COMMAND
				exit 0
				;;
 			*) break ;;
		esac
	done
	
	SAMPLE=$1
}

##########################################################################################
# RUNNING COMMAND ACTION
##########################################################################################

ngsCmd_INIT() {
	if $SE; then prnCmd "# BEGIN: INIT SINGLE-END"
	else prnCmd "# BEGIN: INIT PAIRED-END"; fi
	
    # make relevant directory
	if [ ! -d $SAMPLE/init ]; then 
		prnCmd "mkdir $SAMPLE/init"
		if ! $DEBUG; then mkdir $SAMPLE/init; fi 
	fi
	
    # unzip raw files to init subdirectory. Assumes contains
    # the original compressed raw files
	prnCmd "zcat $ngsLocal_INIT_INP_DIR/$SAMPLE/*_R1_* > $SAMPLE/init/unaligned_1.fq"
	if ! $DEBUG; then 
		zcat $ngsLocal_INIT_INP_DIR/$SAMPLE/*_R1_* > $SAMPLE/init/unaligned_1.fq
	fi
	
	if ! $SE; then 
        # paired-end
		prnCmd "zcat $ngsLocal_INIT_INP_DIR/$SAMPLE/*_R2_* > $SAMPLE/init/unaligned_2.fq;"
		if ! $DEBUG; then 
			zcat $ngsLocal_INIT_INP_DIR/$SAMPLE/*_R2_* > $SAMPLE/init/unaligned_2.fq
		fi
	fi
	
	# run error checking
	if ! $DEBUG; then ngsErrorChk_INIT $@; fi

	if $SE; then prnCmd "# FINISHED: INIT SINGLE-END"
	else prnCmd "# FINISHED: INIT PAIRED-END"; fi
}

##########################################################################################
# ERROR CHECKING. Confirm that the input files are not empty and if PE
# then make sure the files have the same number of lines.
##########################################################################################

ngsErrorChk_INIT() {
	prnCmd "# INIT ERROR CHECKING: RUNNING"

	inputFile_1="$ngsLocal_INIT_INP_DIR/$SAMPLE/*_R1_*"
	outputFile_1="$SAMPLE/init/unaligned_1.fq"

	# make sure expected output file exists
	if [ ! -f $outputFile_1 ]; then
		errorMsg="Expected INIT output file does not exist.\n"
		errorMsg+="\tinput file: $inputFile_1\n"
		errorMsg+="\toutput file: $outputFile_1\n"
		prnError "$errorMsg"
	fi

	# compute number of lines in first read file
	mate1=`wc -l $outputFile_1 | awk '{print $1}'`

	# make sure first read file isn't empty
	if [ "$mate1" -eq "0" ]; then
		errorMsg="The first reads file is empty after uncompressing from the raw directory.\n"
		errorMsg+="\tinput file: $inputFile_1\n"
		errorMsg+="\toutput file: $outputFile_1\n"
		prnError "$errorMsg"
	fi

	# if there are fewer than 5,000 reads in input file then BLAST will fail
	if [ "$mate1" -lt "5000" ]; then
		warningMsg="The first reads file contains fewer than 5,000 reads.\n"
		warningMsg+="This will cause the BLAST module to crash.\n"
		warningMsg+="If you are not using the BLAST module then you can safely ignore this warning.\n"
		warningMsg+="\tinput file: $inputFile_1\n"
		warningMsg+="\toutput file: $outputFile_1\n"
		prnWarning "$warningMsg"
	fi

	if ! $SE; then
		# paired-end
		inputFile_2="$ngsLocal_INIT_INP_DIR/$SAMPLE/*_R2_*"
		outputFile_2="$SAMPLE/init/unaligned_2.fq"

		# make sure expected output file exists
		if [ ! -f $outputFile_2 ]; then
			errorMsg="Expected INIT output file does not exist.\n"
			errorMsg+="\tinput file: $inputFile_2\n"
			errorMsg+="\toutput file: $outputFile_2\n"
			prnError "$errorMsg"
		fi

		# compute number of lines in second read file
		mate2=`wc -l $outputFile_2 | awk '{print $1}'`

		# make sure first and second read files have same number of lines
		if [ "$mate1" -ne "$mate2" ]; then
			errorMsg="Read files do not have the same number of lines after uncompressing from the raw directory.\n"
			errorMsg+="\tnum lines in first read file: $mate1\n"
			errorMsg+="\tinput file: $inputFile_1\n"
			errorMsg+="\toutput file: $outputFile_1\n\n"
			errorMsg+="\tnum lines in second read file: $mate2\n"
			errorMsg+="\tinput file: $inputFile_2\n"
			errorMsg+="\toutput file: $outputFile_2\n"
			prnError "$errorMsg"
		fi
	fi

	prnCmd "# INIT ERROR CHECKING: DONE"
}