dge_utils.sh

## docs
## http://blog.joncairns.com/2013/08/what-you-need-to-know-about-bash-functions/

## define common binaries
if [ $(hostname) == "bioinformatics-srv1" ]; then
    export BIO_BIN_BASE="/local/home/brandl/bin"
else
    export BIO_BIN_BASE="/projects/bioinfo/holger/bin"
fi

export PATH=${BIO_BIN_BASE}/bowtie2-2.2.5:$PATH
export PATH=${BIO_BIN_BASE}/deepTools-2.2.2/bin:$PATH
export PATH=${BIO_BIN_BASE}/FastQC_0.11.2:$PATH
export PATH=${BIO_BIN_BASE}/bedtools2-2.25.0/bin/:$PATH
export PATH=${BIO_BIN_BASE}/samtools-1.3:$PATH
export PATH=${BIO_BIN_BASE}/STAR-2.5.1b/source:$PATH
export PATH=${BIO_BIN_BASE}/ucsc:$PATH # for wigToBigWig
#export PATH=/home/brandl/bin/subread-1.4.6-p3-Linux-x86_64/bin:$PATH


## add cluster job manager
export PATH=/projects/bioinfo/tools/joblist_v0.7:$PATH

## makd sure that rend.R is present
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.23/R/rendr/rendr_utils.sh 2>&1 2>/dev/null)


## backward compatibility wrappers for old shell cluster utils
#joblist(){
#  jl add $*
#}
#export -f joblist
#
#
#wait4jobs(){
#  jl wait $*
#}
#export -f wait4jobs


# which tophat;  which bowtie2; which cuffdiff

mcdir(){
    if [ ! -d "$1" ]; then
        mkdir "$1";
    fi;

    cd "$1";
}
export -f mcdir


mailme(){
    echo "Subject:"$1 "$2" | sendmail -v $(whoami)@mpi-cbg.de > /dev/null ;
}
export -f mailme


ziprm(){
    if [ $# -lt 2 ]; then echo "Usage: ziprm <tarbasename> [<file>]+"; return; fi

    tarName=$(date +'%y%m%d')_"$1".tar.gz; shift
    tar czf $tarName $@; rm $@;
}
export -f ziprm



## no longer needed because packages are no kept in home
#export R_LIBS=/tmp/r_index ## export to make sure that packages are load from local repository, otherwise sqlite won't work


## create fastq report for all fastq and fastq.gz files in the current directory
dge_fastqc(){

while getopts "o:" curopt; do
    case $curopt in
    o) outputDir=$OPTARG;
    esac
done
shift $(($OPTIND - 1))

local fastqFiles=$*

#if [ -z "$fastqFiles" ]; then
if [ $# -lt 1 ]; then
     echo "Usage: dge_fastqc [-o <output_directory>] [<fastq.gz file>]+" >&2 ; return;
fi

## use current directory if not specified
if [ -z "$outputDir" ]; then
     outputDir="fastqc"
fi

if [ ! -d "$outputDir" ]; then
    echo "creating output directory '$outputDir'"
    mkdir $outputDir
fi


for fastqFile in $fastqFiles ; do
    echo "fastqcing $fastqFile"

    if [ ! -f $fastqFile ]; then
        continue;
    fi
    
    jl submit -j .fastqc_jobs -q medium -n "fastqc__$(basename $fastqFile)" "fastqc -j ${JAVA_HOME}/bin/java -o $outputDir -f fastq $fastqFile"
done

jl wait --report .fastqc_jobs

rend.R ${NGS_TOOLS}/misc/fastqc_summary.R $outputDir

mailme "$project: fastqc done in $(pwd)"

}
export -f dge_fastqc


dge_bam_correlate(){

if [ $# -eq 0 ]; then
    echo "Usage: dge_bam_correlate <bam_directory>" >&2 ;
    echo "Usage: dge_bam_correlate <bam_files...>" >&2 ;
    return;
fi


if [ $# -eq 1 ]; then
    bamFiles=$(find $1 | grep ".bam$" | grep -v "unmapped" | sort)
else
    bamFiles=$*
fi

local bamLabels=$(echo "$bamFiles" | xargs -n1 basename | sed 's!.*/!!' | sed 's/_mmf.bam//g' |  sed 's/_ca.bam//g' | sed 's/.bam//g' | xargs echo);
echo "Used bam labels are: $bamLabels"


## see how well bam files correlate using untrimmed data
# http://deeptools.readthedocs.org/en/latest/content/tools/multiBamSummary.html
# http://deeptools.readthedocs.org/en/latest/content/tools/plotCorrelation.html?highlight=plotfile
bcCmd="
## todo add python2 ~/.local/bin/ or fix setup
multiBamSummary bins --bamfiles $(echo $bamFiles | xargs echo) --labels $bamLabels -out bam_cor_matrix.txt --numberOfProcessors 4
plotCorrelation --corData bam_cor_matrix.txt --plotFile bc.pdf --corMethod spearman --zMin 0.5 --zMax 1 -p heatmap
"
#echo "cmd is $bcCmd"
#mysub "${project}__bamcorrelate" "$bcCmd"  -q long -n 4 -R span[hosts=1] | blockScript .bamcorrelate

## old lsf version
#jl submit --wait --jl .bamcorrelate -q long -t 4 -n "${project}__bamcorrelate" "$bcCmd"
jl reset .bamcorrelate
jl submit --jl .bamcorrelate -w 10:00 -t 4 -n "${project}__bamcorrelate" "$bcCmd"
}

export -f dge_bam_correlate


dge_bigwig(){

usage="Usage: dge_bigwig <genome_fai> [<bam_file>]+"


if [ $# -lt 2 ]; then
    echo ${usage} >&2 ; return;
fi

#bamFiles=$(find . -name "*.bam" | grep -v unmapped |  xargs echo)
genomeFai=$1
bamFiles="${@:2}"

if [ ! -f "${genomeFai}" ]; then
    echo "could not find fai index $1! ${usage}" >&2 ; return;
fi

## add bigwig to PATH
export PATH=~/bin:${PATH}

if [ -z "$(which wigToBigWig 2>/dev/null)" ]; then
    echo "could not find wigToBigWig in PATH! ${usage}" >&2 ; #return;
fi

## create big wig files
for bamFile in $bamFiles; do
    sample=$(basename $bamFile .bam)
    echo "converting $bamFile to bigwig format"

    jl submit -j .bigwig -w 10:00 -n "${project}__bw__${sample}" "genomeCoverageBed -split -bg -ibam $bamFile  -g ${genomeFai} |  wigToBigWig -clip stdin ${genomeFai} ${sample}.bw"
done

jl wait --report .bigwig

}
export -f dge_bigwig

## http://stackoverflow.com/questions/6916856/can-bash-show-a-functions-definition
#type dge_bigwig


## Merge technical replicatews
dge_merge_treps(){

usage="Usage: dge_merge_treps <bam_directory> <comma_sep_biosample_spec>"

if [ $# -ne 2 ]; then
    echo $usage >&2 ; return;
fi


local bam_dir=$1; # bam_dir=$baseDir/mapped_trim/
local bio_reps=$2; # bio_samples="test,lala"

if [ ! -d "$bam_dir" ]; then
    echo "bam file directory does not exist! $usage'" >&2 ; return;
fi

if [ $(echo "$bio_samples" | grep "," | wc -l )  -ne 1 ]; then
    echo "Invalid biosample spec! $usage'" >&2 ; return;
fi

#for sample in aRG bRG N; do
for sample in $(echo $bio_samples | tr ",", " "); do
    # DEBUG sample=Insm1_1103

    ## todo use joblist instead here
    (
    sampleBams=$(find $bam_dir -name '*bam'  | grep -v unmapped | grep $sample)
    echo "merging $sample with $sampleBams"

    ## todo add read-groups to bam files
    if [ 1 -eq $(echo "$sampleBams" | wc -l) ]; then
        cp $sampleBams $sample.bam
    else
        samtools merge - $(echo $sampleBams | xargs echo) | samtools sort - $sample
    fi

    samtools index $sample.bam
    )&
done

}
export -f dge_merge_treps

# Create a star index for a given igenome
dge_create_star_index(){

    if [ $# -ne 1 ]; then
        echo "Usage: dge_create_star_index <igenome>" >&2 ; return;
    fi

    igenome=$1

    if [ ! -d "$igenome" ] | [ ! -d "${igenome}/Sequence" ]; then
        echo "igenome directory '$igenome' does not exist" >&2 ; return;
    fi

    export star_index="${igenome}/Sequence/StarIndex"

    ## stop if index exists already
    if [ -d "$star_index" ]; then
        echo "Error: Index directory ${star_index} already exists." >&2 ; return;
    fi

#    chmod +w $(dirname ${star_index})

    mailme "${project}: creating STAR index in ${star_index}"
    mkdir ${star_index}

    cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 10"
    #eval $cmd
    #STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/Chromosomes/*.fa --runThreadN 10
    jl submit --wait -t 5 -w 10:00 -m 30g -n "${project}_star_index" "$cmd"

    ## prevent further modification
#    chmod -w $(dirname ${star_index})

    mailme "created star index for $igenome"
}
export -f dge_create_star_index


dge_get_pc_isoforms(){
# todo write more generic version that also filtered provided gtf and/or allow for ccds filtering as well

if [ $# -ne 1 ]; then
    echo "Usage: dge_get_pc_isoforms <hsapiens/mmusculus/other_ensembl_species_identifier>" >&2 ; return;
fi

echo '
require(biomaRt)
require(dplyr)
require(ggplot2)

mart <- useDataset(paste0(commandArgs(T)[1], "_gene_ensembl"), mart = useMart("ensembl"))
#mart <- useDataset("hsapiens_gene_ensembl", mart = useMart("ensembl"))
#mart <- useDataset("mmusculus_gene_ensembl", mart = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))

pcTx <- getBM(attributes=c("ensembl_gene_id", "ensembl_transcript_id", "gene_biotype", "transcript_biotype"),  mart=mart) %>%
    filter(transcript_biotype=="protein_coding")

#ggplot(pcTx, aes(gene_biotype)) + geom_bar() + coord_flip()
#ggplot(pcTx, aes(transcript_biotype)) + geom_bar() + coord_flip()cd

#write.table(with(pcTx, data.frame(ensembl_transcript_id)), col.names=F, file="mm10_pc_tx.txt",quote=F,row.names=F)
# just print results to stdout
write.table(with(pcTx, data.frame(ensembl_transcript_id)), col.names=F, file=stdout(),quote=F,row.names=F)
' | Rscript --vanilla - $1 2>/dev/null
}
export -f dge_get_pc_isoforms



dge_star_counts2matrix(){
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.13/R/core_commons.R")

## STAR count file format is
#column 1: gene ID
#column 2: counts for unstranded RNA-seq
#column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes)

exprCounts <- list.files(".", "ReadsPerGene.out.tab") %>% ldply(function(countFile){
    read.delim(countFile, header=F) %>%
        select(V1, V2) %>%
        set_names("ensembl_gene_id", "num_alignments") %>%
        filter(!str_detect(ensembl_gene_id, "^N_")) %>%
        mutate(sample=trim_ext(countFile, ".ReadsPerGene.out.tab"))
}, .progress="text")

countMatrix <- spread(exprCounts, sample, num_alignments)

write.delim(countMatrix, "star_counts_matrix.txt")
' | R --vanilla -q

}
export -f dge_star_counts2matrix