From bc469ff88db83c9cc4f2976c0547c0fdc19365b1 Mon Sep 17 00:00:00 2001
From: Hasindu Gamaarachchi <hasindu2008@gmail.com>
Date: Wed, 4 Oct 2023 15:48:45 +1100
Subject: [PATCH] update test

---
 test/test_extensive.sh     | 50 +++++++++++++++++++++++++++++---------
 test/test_qscore_split2.sh |  2 +-
 2 files changed, 40 insertions(+), 12 deletions(-)

diff --git a/test/test_extensive.sh b/test/test_extensive.sh
index 8baf5e8..583a9b5 100755
--- a/test/test_extensive.sh
+++ b/test/test_extensive.sh
@@ -1,22 +1,37 @@
 #!/bin/bash
 
+# MIT License
+
+# Copyright (c) 2023 Hasindu Gamaarachchi
+# Copyright (c) 2023 James Ferguson
+
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
 die() {
     echo "Error: $@" >&2
     exit 1
 }
 
-instal_venv(){
-    test -d ${PATH_TO_EEL_VENV} && rm -r ${PATH_TO_EEL_VENV}
-    python3.8 -m venv ${PATH_TO_EEL_VENV} || die "Failed to create venv"
-    source ${PATH_TO_EEL_VENV} || die "Failed to source ${PATH_TO_EEL_VENV}"
-    pip install --upgrade pip || die "Failed to upgrade pip"
-    pip install --upgrade setuptools wheel || die "Failed to upgrade setuptools"
-    python setup.py install || die "Failed to install buttery-eel"
-    deactivate
-}
 
 CURRENT_GUPPY=$(grep "ont-pyguppy-client-lib" requirements.txt | cut -d "=" -f 3)
 test -z ${CURRENT_GUPPY} && die "ont-pyguppy-client-lib not found in requirements.txt"
+
 export PATH_TO_GUPPY=/install/ont-guppy-${CURRENT_GUPPY}/bin/
 export GUPPY_OUT_TMP=ont-guppy-tmp
 export EEL_OUT_TMP=buttery_eel_tmp.fastq
@@ -24,10 +39,14 @@ export EEL_OUT_TMP=buttery_eel_tmp.fastq
 
 export PATH_TO_EEL_VENV=./venv3/bin/activate
 
-
 export PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
 export REFIDX=/genome/hg38noAlt.idx
 
+echo "Installation"
+test/test_install.sh || die "test failed"
+echo ""
+echo "********************************************************************"
+
 echo "R9.4.1 DNA - FAST model - 20k reads"
 export PATH_TO_FAST5=/data/slow5-testdata/NA12878_prom_subsubsample/fast5/
 export PATH_TO_BLOW5=/data/slow5-testdata/NA12878_prom_subsubsample/reads.blow5
@@ -36,7 +55,7 @@ test/test.sh || die "test failed"
 echo ""
 echo "********************************************************************"
 
-echo "R10.4.1 DNA - HAC model - 20k reads - split qscore"
+echo "R10.4.1 DNA - HAC model - 20k reads - split qscore inbuilt"
 export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
 export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
 export MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
@@ -44,6 +63,15 @@ test/test_qscore_split.sh || die "test failed"
 echo ""
 echo "********************************************************************"
 
+echo "R10.4.1 DNA - FAST model - 20k reads - split qscore script"
+export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
+export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
+export MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
+test/test_qscore_split2.sh || die "test failed"
+echo ""
+echo "********************************************************************"
+
+
 echo "split reads"
 export OPTS_GUPPY="--detect_mid_strand_adapter --trim_adapters --detect_adapter --do_read_splitting --trim_strategy dna"
 export OPTS_EEL=$OPTS_GUPPY
diff --git a/test/test_qscore_split2.sh b/test/test_qscore_split2.sh
index da88a45..ce23575 100755
--- a/test/test_qscore_split2.sh
+++ b/test/test_qscore_split2.sh
@@ -93,7 +93,7 @@ else
     echo "Memory usage is OK: $MEM"
 fi
 cat eel.log
-/usr/bin/time -v python3 scripts/qscore_split.py ${EEL_OUT_TMP} reads -q 7
+/usr/bin/time -v python3 scripts/split_qscore.py ${EEL_OUT_TMP} reads -q 7
 
 ${PATH_TO_IDENTITY} ${REFIDX} reads.pass.fastq | cut -f 2-> ${EEL_OUT_TMP}.identity