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modify_table.sh
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Wed, Jun 12, 14:52

modify_table.sh
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#!/usr/bin/env bash
#modify_table.sh
# Generic script to modify a table
################
# Main
# Args:
# (1) table_fp Path to comma-delimited txt table (1st row as header)
# (2) method Method tu apply for table modification
# (3) category Name of the column in 'table_fp' that contains data category
# (4) map_fp Path to mapping file
# (5) factor Name of the column in 'map_fp' that contains sorting factor
# (6) output_fp Path to output file
################
main() {
local funcname
funcname='main'
local table_fp
table_fp="${1}"
[[ ! -e "${table_fp}" ]] && err "in ${funcname}() cannot find ${table_fp}"
local method
method="${2}"
if [[ "${method}" == 'check_dataset' ]]; then
local category_column
category_column="${3}"
local map_fp
map_fp="${4}"
local sample_name
sample_name="${5}"
elif [[ "${method}" == 'table2R' ]]; then
local output_fp
output_fp="${3}"
elif [[ "${method}" == 'aggregate' ]]; then
local category_column
category_column="${3}"
local level
level="${4}"
local fun
fun="${5}"
local output_fp
output_fp="${6}"
else
err "in ${funcname}() wrong argument to method (2): ${method}"
fi
# Modify table
if [[ "${method}" == 'check_dataset' ]]; then
verify_format "${table_fp}" "${category_column}" "${map_fp}" "${sample_name}"
elif [[ "${method}" == 'check_map' ]]; then
verify_map_format "${table_fp}"
elif [[ "${method}" == 'table2R' ]]; then
remove_comments "${table_fp}" "${output_fp}" # remove any comment lines at the begining of the table and the 1st element of the 1st line
elif [[ "${method}" == 'aggregate' ]]; then
aggregate_by_category_level "${table_fp}" "${category}" "${level}" "${fun}" "${output_fp}"
fi
return 0
}
set -o nounset
set -o pipefail
#set -o xtrace
__dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
__file="${__dir}/$(basename "${BASH_SOURCE[0]}")"
__base="$(basename ${__file})"
__lib="${__dir}"/../lib
source "${__lib}"/genocrunchlib.sh
__user=$(basename "${HOME}")
__workingdir="$(pwd)"
[[ ! -w "${__workingdir}" ]] && err "(line ${LINENO}) write permission denied on ${__workingdir}"
__roottmp=/tmp
if ([[ ! -d "${__roottmp}" ]] || [[ ! -w "${__roottmp}" ]]) ; then
__roottmp="${__dir}"/../tmp
[[ ! -d "${__roottmp}" ]] && { mkdir "${__roottmp}" ; [[ "$?" -ne 0 ]] && \
err "(line ${LINENO}) cannot make ${__roottmp}" ; }
fi
tmpdir=$(mktemp -d "${__roottmp}"/"$(basename ${__file} .sh)"XXX)
trap 'rm -rf "${tmpdir}"' EXIT # makes sure tmpdir is deleted when exit
[[ ! -d "${tmpdir}" ]] && { mkdir "${tmpdir}" ; [[ "$?" -ne 0 ]] && \
err "(line ${LINENO}) cannot make ${tmpdir}" ; }
[[ ! -w "${tmpdir}" ]] && err "(line ${LINENO}) write permission denied on ${tmpdir}"
chown "${__user}" "${tmpdir}"
main "${@}"
exit 0

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