add: bin folder for nextflow

src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/CURRENT

+MANIFEST-000002

src/primingprob/bin/.nextflow/history

+2021-12-30 14:13:27	4.4s	curious_bose	ERR	0451f3cb7c837de5727f9314aa3308b7	7a063d50-5a1e-4286-aa35-9883474713bf	nextflow run RIblast_process4.nf

src/primingprob/bin/cli_priming_prob.py

+"""Command-line interface client."""
+import argparse
+import os
+from pathlib import Path
+import sys
+from src.primingprob.priming_prob import Probability as Pbt  # type: ignore
+
+
+def parse_args():
+    """Parse CLI arguments.
+
+    Returns:
+        Parsed CLI arguments.
+    """
+    parser = argparse.ArgumentParser(
+        description="RIblast input",
+        add_help=False,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+
+    parser.add_argument(
+        'input_file',
+        type=lambda p: Path(p).absolute(),
+        metavar="PATH",
+        help="path to energy-file",
+    )
+
+    parser.add_argument(
+        'fasta_file',
+        type=lambda p: Path(p).absolute(),
+        metavar="PATH",
+        help="path to fasta-file",
+    )
+
+    parser.add_argument(
+        'output_file',
+        type=lambda p: Path(p).absolute(),
+        metavar="PATH",
+        help="path to output-file",
+    )
+
+    return parser.parse_args()
+
+
+def main():
+    """Start priming_prob.py."""
+    args = parse_args()
+
+    if os.path.exists(args.input_file) and os.path.exists(args.fasta_file):  # pragma: no cover
+        paradata = Pbt.inter_para(args.input_file)
+        Pbt.inter_prob(paradata, args.fasta_file, args.output_file)
+
+    if not os.path.exists(args.input_file) and os.path.exists(args.fasta_file):  # pragma: no cover
+        sys.exit("Path to input-file does not exist")
+
+
+def init():
+    """Entry point for CLI executable."""
+    if __name__ == '__main__':
+        main()
+
+
+init()

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err

+/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh: line 2: RIblast: command not found

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run

+#!/bin/bash
+# NEXTFLOW TASK: RIblast_interaction
+set -e
+set -u
+NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
+NXF_ENTRY=${1:-nxf_main}
+
+
+nxf_date() {
+    local ts=$(date +%s%3N);
+    if [[ ${#ts} == 10 ]]; then echo ${ts}000
+    elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
+    elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
+    elif [[ ${#ts} == 13 ]]; then echo $ts
+    else echo "Unexpected timestamp value: $ts"; exit 1
+    fi
+}
+
+nxf_env() {
+    echo '============= task environment ============='
+    env | sort | sed "s/\(.*\)AWS\(.*\)=\(.\{6\}\).*/\1AWS\2=\3xxxxxxxxxxxxx/"
+    echo '============= task output =================='
+}
+
+nxf_kill() {
+    declare -a children
+    while read P PP;do
+        children[$PP]+=" $P"
+    done < <(ps -e -o pid= -o ppid=)
+
+    kill_all() {
+        [[ $1 != $$ ]] && kill $1 2>/dev/null || true
+        for i in ${children[$1]:=}; do kill_all $i; done
+    }
+
+    kill_all $1
+}
+
+nxf_mktemp() {
+    local base=${1:-/tmp}
+    if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX
+    else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX
+    fi
+}
+
+on_exit() {
+    exit_status=${nxf_main_ret:=$?}
+    printf $exit_status > /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode
+    set +u
+    [[ "$tee1" ]] && kill $tee1 2>/dev/null
+    [[ "$tee2" ]] && kill $tee2 2>/dev/null
+    [[ "$ctmp" ]] && rm -rf $ctmp || true
+    exit $exit_status
+}
+
+on_term() {
+    set +e
+    [[ "$pid" ]] && nxf_kill $pid
+}
+
+nxf_launch() {
+    /bin/bash -ue /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh
+}
+
+nxf_stage() {
+    true
+    # stage input files
+    rm -f transcript.fasta
+    rm -f primer.fasta
+    ln -s /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/transcript.fasta transcript.fasta
+    ln -s /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/primer.fasta primer.fasta
+}
+
+nxf_unstage() {
+    true
+    [[ ${nxf_main_ret:=0} != 0 ]] && return
+}
+
+nxf_main() {
+    trap on_exit EXIT
+    trap on_term TERM INT USR2
+    trap '' USR1
+
+    [[ "${NXF_CHDIR:-}" ]] && cd "$NXF_CHDIR"
+    NXF_SCRATCH=''
+    [[ $NXF_DEBUG > 0 ]] && nxf_env
+    touch /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.begin
+    set +u
+    set -u
+    [[ $NXF_SCRATCH ]] && echo "nxf-scratch-dir $HOSTNAME:$NXF_SCRATCH" && cd $NXF_SCRATCH
+    nxf_stage
+
+    set +e
+    local ctmp=$(set +u; nxf_mktemp /dev/shm 2>/dev/null || nxf_mktemp $TMPDIR)
+    local cout=$ctmp/.command.out; mkfifo $cout
+    local cerr=$ctmp/.command.err; mkfifo $cerr
+    tee .command.out < $cout &
+    tee1=$!
+    tee .command.err < $cerr >&2 &
+    tee2=$!
+    ( nxf_launch ) >$cout 2>$cerr &
+    pid=$!
+    wait $pid || nxf_main_ret=$?
+    wait $tee1 $tee2
+    nxf_unstage
+}
+
+$NXF_ENTRY

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh

+#!/bin/bash -ue
+RIblast db -i transcript.fasta -o test_db
+RIblast ris -i primer.fasta -o Energies.txt -d test_db

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode

+127
\ No newline at end of file

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta

+/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/primer.fasta
\ No newline at end of file

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta

+/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/transcript.fasta
\ No newline at end of file