Break up GTR into module and submodules
This commit is contained in:
@@ -1,7 +1,7 @@
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#!/usr/bin/env bash
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# Copyright 2024 Bryan C. Roessler
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#
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# This is a code scratchpad for organizing the Hartman Lab Server workflow
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# This is a flexible yet opinionated analysis workflow for the Hartman Lab
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# It contains a mixture of code/pseudocode and shouldn't be run until this message is removed
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#
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# Allow indirect functions
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@@ -14,6 +14,7 @@
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# @option -p<value> | --project=<value> Include one or more projects in the analysis
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# @option -i<value> | --include=<value> Include one or more modules in the analysis (default: all modules)
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# @option -x<value> | --exclude=<value> Exclude one or more modules in the analysis
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# @option -m | --markdown Generate the shdoc markdown file for this program
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# @option -y | --yes | --auto Assume yes answer to all questions (non-interactive mode)
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# @option -d | --debug Turn on extra debugging output
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# @option -h | --help Print help message and exit (overrides other options)
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@@ -49,6 +50,8 @@ print_help() {
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If no --include is specified, all modules are run
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--exclude, -x MODULE
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See MODULES section below for list of modules to exclude
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--markdown, -m
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Generate the shdoc markdown file for this program
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--yes, -y, --auto
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Always answer yes to questions (non-interactive mode)
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--debug, -d
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@@ -86,8 +89,8 @@ print_help() {
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parse_input() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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long_opts="project:,include:,exclude:,yes,auto,debug,help"
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short_opts="+p:i:x:yhd"
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long_opts="project:,include:,exclude:,markdown,yes,auto,debug,help"
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short_opts="+p:i:x:mydh"
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if input=$(getopt -o $short_opts -l $long_opts -- "$@"); then
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eval set -- "$input"
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@@ -117,6 +120,9 @@ parse_input() {
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EXCLUDE_MODULES+=("$1")
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fi
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;;
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--markdown|-m)
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documentation
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;;
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--yes|-y|--auto)
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declare -g YES=1
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;;
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@@ -176,8 +182,9 @@ debug() { (( DEBUG )) && echo "Debug: $*"; }
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# @section Modules
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# @description A module contains a cohesive set of actions/experiments to run on a project
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# Use a module when:
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# * Building a new type of analysis
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# * Combining submodules
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# * Building a new type of analysis from scratch
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# * Generates project directories
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# * Can combine other modules and submodules
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#
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#
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@@ -327,13 +334,13 @@ qhtcp() {
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# Our list of submodules (functions) to run for this module
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# Put these in the appropriate order of operations
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submodules=(
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modules=(
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r_join_interact
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java_extract
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r_add_shift_values
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r_heat_maps_zscores
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r_heat_maps_homology
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py_gtf
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gtf
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r_compile_gtf
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)
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@@ -364,12 +371,31 @@ qhtcp() {
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pushd "$QHTCP_DIR/REMc" || return 1
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# Run each submodule
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for s in "${submodules[@]}"; do "$s"; done
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for s in "${modules[@]}"; do "$s"; done
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popd || return 1
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}
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module gtf
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# @section GTF
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# @description GTF module for QHTCP
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gtf() {
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debug "Running: ${FUNCNAME[0]}"
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process_dir="GTF/Process"
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function_dir="GTF/Function"
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component_dir="GTF/Component"
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py_gtf "$process_dir"
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# Perform operations in each directory in parallel
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for d in "$process_dir" "$function_dir" "$component_dir"; do
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rsync -a "$process_dir/REMcRdy_lm_only" "$d"/
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out_file="${d##*/}Results.txt" # Use the dirname to create each Results filename
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pl_gtf "$d" "$out_file" & # parallelize
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done
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}
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# @section Submodules
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# @description Submodules provide functionaility to modules and are reusable between modules
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# Use a submodule when:
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@@ -474,25 +500,25 @@ r_heat_maps_homology() {
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submodule py_gtf
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# @description Perform GTF
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# @description Perform python portion of GTF
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# @arg $1 string Directory to process
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py_gtf() {
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debug "Running: ${FUNCNAME[0]}"
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process_dir="GTF/Process"
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function_dir="GTF/Function"
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component_dir="GTF/Component"
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in_file="REMcRdy_lm_only.csv-finalTable.csv"
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out_file="$process_dir/REMcRdy_lm_only/1-0-0-finaltable.csv"
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echo "$PYTHON DconJG2.py $in_file $process_dir/"
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"$PYTHON" DconJG2.py "$in_file" "$process_dir/"
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out_file="$1/REMcRdy_lm_only/1-0-0-finaltable.csv"
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debug "$PYTHON DconJG2.py $in_file $1/"
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"$PYTHON" DconJG2.py "$in_file" "$1/"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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unset out_file
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rsync -a "$process_dir/REMcRdy_lm_only" GTF/Function/
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rsync -a "$process_dir/REMcRdy_lm_only" GTF/Component/
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}
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# @description Not sure what to name this
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# @arg $1 string directory name
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_process() {
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submodule pl_gtf
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# @description Perl module for GTF
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# @arg $1 string working directory
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# @arg $2 string output file
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pl_gtf() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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set1="ORF_List_Without_DAmPs.txt"
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pushd "$1" || return 1
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shopt -s nullglob
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@@ -500,28 +526,21 @@ py_gtf() {
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shopt -u nullglob
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for s in "${set2[@]}"; do
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debug "pl_analyze $set1 $s"
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pl_analyze "$set1" "$s"
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debug "pl_terms2tsv $s"
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pl_terms2tsv "$s"
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"$PERL" terms2tsv_v4.pl "$s.terms" > "$s.tsv"
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done
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# Concat the process ontology outputs from the /REMcReady_lm_only folder
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echo "$PYTHON Concatenate_GTF_results.py REMcRdy_lm_only/ $out_file"
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echo "$PYTHON Concatenate_GTF_results.py REMcRdy_lm_only/ $2"
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echo "TODO: Concatenate_GTF_results.py should be translated to bash"
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"$PYTHON" Concatenate_GTF_results.py REMcRdy_lm_only/ "$out_file"
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"$PYTHON" Concatenate_GTF_results.py REMcRdy_lm_only/ "$2"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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[[ -f $2 ]] || (echo "$2 does not exist"; return 1)
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popd || return 1
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}
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# Perform operations in each directory
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for d in "$process_dir" "$function_dir" "$component_dir"; do
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set1="ORF_List_Without_DAmPs.txt"
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out_file="${d##*/}Results.txt" # Use the dirname to create each Results filename
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_process "$d" & # parallelize
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done
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}
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submodule pl_analyze
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# @description Perl analyze submodule
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@@ -550,23 +569,7 @@ pl_terms2tsv() {
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}
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submodule documentation
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# @section Documentation
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# @description Generates markdown documentation from this script using shdoc
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documentation() {
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debug "Running: ${FUNCNAME[0]}"
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# Print markdown to stdout
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shdoc < "$SCRIPT"
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# Create markdown file
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shdoc < "$SCRIPT" > documentation.md
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}
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submodule r_compile_gtf
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# @description Compile GTF in R
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r_compile_gtf() {
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debug "Running: ${FUNCNAME[0]}"
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@@ -575,6 +578,18 @@ r_compile_gtf() {
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}
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submodule documentation
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# @section Documentation
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# @description Generates markdown documentation from this script using shdoc
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documentation() {
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debug "Running: ${FUNCNAME[0]}"
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# Print markdown to stdout
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((DEBUG)) && shdoc < "$SCRIPT"
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# Create markdown file
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shdoc < "$SCRIPT" > documentation.md
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}
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# @description The main loop of script-run-workflow
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# May eventually need to add git ops
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# Passes on arguments
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