bash_snippets

bash scripts for daily use

counts

#!/bin/bash
# output occurences in descending order
# SK
sort <&0 | uniq -c | sort -nr

texit

#!/bin/bash
# pdflatex either all .tex files or only <file>[.[tex]]

if [ $# == 0 ]; then
    T=(*.tex)
    if [ "${T[0]}" == "*.tex" ]; then
        echo 'No .tex files here!' >&2
        exit 1
    fi
else
    T=("${1%.*}.tex")
    if [ ! -f "$T" ]; then
        echo "No file named $T here!" >&2
        exit 1
    fi
fi
for F in ${T[@]}; do
    B=${F%.*}
    pdflatex "$B"
    if [ -f "${B}.aux" ]; then
        bibtex "$B" && pdflatex "$B"
    fi
    pdflatex "$B"
done

bamify

#!/bin/bash
# bamify - select mapped reads, sort, convert to bam and index
# by Sebastian Krautwurst

if [ -z "$1" ]
then
    echo "No input sam file(s) given!"
    exit
fi

while [ ! -z "$1" ]
do
    echo -n "$1"
    BAM="${1%.sam}".bam
    samtools view -h -F4 "$1" | samtools sort | samtools view -hb > "$BAM" && samtools index "$BAM"
    echo " bamified to $BAM"
    shift
done

plotify

#!/bin/bash
# plotify - minimap2 some reads ($2,$3,...) to some reference ($1) and plot the coverage
# by Sebastian Krautwurst

if [ -z "$1" ]
then
    echo "No input given!"
    exit 1
elif [ -z "$2" ]
then
    echo "No input reads given!"
    exit 1
fi

REF="$1"
shift

while [ ! -z "$1" ]
do
    echo "Plotify $1 ..."
    BN=$(basename "$1")
    BAM="${BN}".bam
    minimap2 -ax map-ont "$REF" "$1" | samtools view -h -F4 | samtools sort | samtools view -hb > "$BAM" && samtools index "$BAM"
    echo "Mapped $1 and bamified to $BAM"
    plotCoverageExons.py -o "${BAM%.*}.pdf" "$BAM"
    echo "Plotted coverage to ${BAM%.*}.pdf"
    shift
done