bash snippets

snippets.sh

###########################################################################################################################
# commands
###########################################################################################################################

# ls only file size and name
stat -c "%s %n" *.txt | column -t

# watch output of qstat, highlight changes every 5s
watch -n 5 -d 'qstat'

# grep last occurrence of "%" in all logfiles in folder, watch result with highlighting
watch -d -n 10 'for file in *.log; do tac ${file} | grep -m1 %; done'

# create TAR of all PNG files in folder recursively
find thepath/ -name \*.png | tar -cf pngs.tar -T -

# print short hash of current Git commit
git log --pretty=format:'%h' -n 1

# given samples.txt, save TSV (w/ header) of {sample name, BAM file location}
fiss annot_get WorkspaceName sample=`cat samples.txt | paste -sd ','` clean_bam_file_capture > bams.tsv

# match row of TSV by value of any column, retrieve value of second column
sample="asdf"
fcid=`cat bams.tsv | grep $sample | cut -f2`

# given TSV (w/ header) of {sample_id, target file location}, copy target files to local dir
cat targets.tsv | cut -f 2 | tail -n +2 | xargs cp -t targets/

# print list of column headers in TSV
cat file.tsv | grep -v "^#" | head -n 1 | tr '\t' '\n'

###########################################################################################################################
# functions/bash_login utils
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# fresh R session
alias Rscript="Rscript --no-save --no-restore"
alias R="R --no-save --no-restore"

# print head, tail, and head...tail of TSV file
function thead() {
  cat $1 | grep -v "^#" | head | column -t
}

function ttail() {
  tail $1 | column -t
}

function tht() {
  { cat $1 | grep -v "^#" | head; echo -e "\e[35m...\e[39m"; tail $1; } | column -t
}

# print unique entries in column <i> of TSV file
# c 3 file.tsv
function c() {
  cat $2 | grep -v "^#" | cut -f $1 | uniq
}

# colorized `man` output
man() {
  env \
  LESS_TERMCAP_mb=$(printf "\x1b[38;2;255;200;200m") \
  LESS_TERMCAP_md=$(printf "\x1b[38;2;255;100;200m") \
  LESS_TERMCAP_me=$(printf "\x1b[0m") \
  LESS_TERMCAP_so=$(printf "\x1b[38;2;60;90;90;48;2;40;40;40m") \
  LESS_TERMCAP_se=$(printf "\x1b[0m") \
  LESS_TERMCAP_us=$(printf "\x1b[38;2;150;100;200m") \
  LESS_TERMCAP_ue=$(printf "\x1b[0m") \
  man "$@"
}