From 6171438b393e0fe8f3a5b5f51612cda161ac5019 Mon Sep 17 00:00:00 2001
From: Melvin Alappat <melvin.alappat@unibas.ch>
Date: Thu, 30 Dec 2021 14:22:33 +0100
Subject: [PATCH] add: bin folder for nextflow
---
.../db/CURRENT | 1 +
.../db/LOCK | 0
.../db/MANIFEST-000002 | Bin 0 -> 50 bytes
.../index.curious_bose | Bin 0 -> 17 bytes
src/primingprob/bin/.nextflow/history | 1 +
src/primingprob/bin/cli_priming_prob.py | 63 ++++++++++
.../.command.begin | 0
.../.command.err | 1 +
.../.command.out | 0
.../.command.run | 108 ++++++++++++++++++
.../.command.sh | 3 +
.../e44fcf5a9b873853ca63a43b531eb0/.exitcode | 1 +
.../primer.fasta | 1 +
.../transcript.fasta | 1 +
14 files changed, 180 insertions(+)
create mode 100644 src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/CURRENT
create mode 100644 src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/LOCK
create mode 100644 src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/MANIFEST-000002
create mode 100644 src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/index.curious_bose
create mode 100644 src/primingprob/bin/.nextflow/history
create mode 100644 src/primingprob/bin/cli_priming_prob.py
create mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.begin
create mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err
create mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.out
create mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run
create mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh
create mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode
create mode 120000 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta
create mode 120000 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta
diff --git a/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/CURRENT b/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/CURRENT
new file mode 100644
index 0000000..1a84852
--- /dev/null
+++ b/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/CURRENT
@@ -0,0 +1 @@
+MANIFEST-000002
diff --git a/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/LOCK b/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/LOCK
new file mode 100644
index 0000000..e69de29
diff --git a/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/MANIFEST-000002 b/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/db/MANIFEST-000002
new file mode 100644
index 0000000000000000000000000000000000000000..bbbc585686bcbcc33686059c69d80b7b4e1291cd
GIT binary patch
literal 50
zcmWIhx#Ncn10$nUPHI_dPD+xVQ)NkNd1i5{bAE0?Vo_pAe$kRS-TOEg7@3$k8JJmE
F7y#sj5K{mE
literal 0
HcmV?d00001
diff --git a/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/index.curious_bose b/src/primingprob/bin/.nextflow/cache/7a063d50-5a1e-4286-aa35-9883474713bf/index.curious_bose
new file mode 100644
index 0000000000000000000000000000000000000000..8c72049dfdc87edc90c895e431634b262f95cc78
GIT binary patch
literal 17
YcmXqe;(tDBcDqIJspKWr!EzfI07;?;Z2$lO
literal 0
HcmV?d00001
diff --git a/src/primingprob/bin/.nextflow/history b/src/primingprob/bin/.nextflow/history
new file mode 100644
index 0000000..dfc43c6
--- /dev/null
+++ b/src/primingprob/bin/.nextflow/history
@@ -0,0 +1 @@
+2021-12-30 14:13:27 4.4s curious_bose ERR 0451f3cb7c837de5727f9314aa3308b7 7a063d50-5a1e-4286-aa35-9883474713bf nextflow run RIblast_process4.nf
diff --git a/src/primingprob/bin/cli_priming_prob.py b/src/primingprob/bin/cli_priming_prob.py
new file mode 100644
index 0000000..198235f
--- /dev/null
+++ b/src/primingprob/bin/cli_priming_prob.py
@@ -0,0 +1,63 @@
+"""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()
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.begin b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.begin
new file mode 100644
index 0000000..e69de29
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err
new file mode 100644
index 0000000..49b6c12
--- /dev/null
+++ b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err
@@ -0,0 +1 @@
+/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh: line 2: RIblast: command not found
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.out b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.out
new file mode 100644
index 0000000..e69de29
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run
new file mode 100644
index 0000000..f21b88e
--- /dev/null
+++ b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run
@@ -0,0 +1,108 @@
+#!/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
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh
new file mode 100644
index 0000000..ea89100
--- /dev/null
+++ b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh
@@ -0,0 +1,3 @@
+#!/bin/bash -ue
+RIblast db -i transcript.fasta -o test_db
+RIblast ris -i primer.fasta -o Energies.txt -d test_db
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode
new file mode 100644
index 0000000..405e057
--- /dev/null
+++ b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode
@@ -0,0 +1 @@
+127
\ No newline at end of file
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta
new file mode 120000
index 0000000..3c8fce8
--- /dev/null
+++ b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta
@@ -0,0 +1 @@
+/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/primer.fasta
\ No newline at end of file
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta
new file mode 120000
index 0000000..cbf803b
--- /dev/null
+++ b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta
@@ -0,0 +1 @@
+/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/transcript.fasta
\ No newline at end of file
--
GitLab