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change paths to dorado_new
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@Psy-Fer
Psy-Fer committed Sep 4, 2024
1 parent ea044c7 commit fc16ccf
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 deletions test/dorado_new/test_extensive.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ die() {
rm -f *.log

echo "Installation"
test/dorado/test_install.sh &> install.log || die "test failed. see install.log for details"
test/dorado_new/test_install.sh &> install.log || die "test failed. see install.log for details"
echo ""
echo "********************************************************************"

Expand All @@ -52,23 +52,23 @@ 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
export MODEL=dna_r9.4.1_450bps_fast.cfg
test/dorado/test.sh &> r9_dna_fast.log || die "test failed. see r9_dna_fast.log for details"
test/dorado_new/test.sh &> r9_dna_fast.log || die "test failed. see r9_dna_fast.log for details"
echo ""
echo "********************************************************************"

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.cfg
test/dorado/test_qscore_split.sh &> r10_split1.log || die "test failed. see r10_split1.log for details"
test/dorado_new/test_qscore_split.sh &> r10_split1.log || die "test failed. see r10_split1.log for details"
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.cfg
test/dorado/test_qscore_split2.sh &> r10_split2.log || die "test failed. See r10_split2.log for details"
test/dorado_new/test_qscore_split2.sh &> r10_split2.log || die "test failed. See r10_split2.log for details"
echo ""
echo "********************************************************************"

Expand All @@ -82,7 +82,7 @@ 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 OPTS_GUPPY="--trim_adapters"
export OPTS_EEL=$OPTS_GUPPY
test/dorado/test.sh &> r10_adaptertrim.log || echo "test failed. See r10_adaptertrim.log for details"
test/dorado_new/test.sh &> r10_adaptertrim.log || echo "test failed. See r10_adaptertrim.log for details"
unset OPTS_GUPPY
unset OPTS_EEL
echo ""
Expand All @@ -93,7 +93,7 @@ echo "********************************************************************"
# export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
# export OPTS_GUPPY="--do_read_splitting --min_score_read_splitting 50"
# export OPTS_EEL=$OPTS_GUPPY
# test/dorado/test.sh &> r10_readsplit.log || echo "test failed. See r10_readsplit.log for details"
# test/dorado_new/test.sh &> r10_readsplit.log || echo "test failed. See r10_readsplit.log for details"
# unset OPTS_GUPPY
# unset OPTS_EEL
# echo ""
Expand All @@ -104,7 +104,7 @@ echo "********************************************************************"
# export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
# export OPTS_GUPPY="--detect_mid_strand_adapter --trim_adapters --detect_adapter --min_score_adapter 60 --do_read_splitting --min_score_read_splitting 50"
# export OPTS_EEL=$OPTS_GUPPY
# test/dorado/test.sh &> r10_readsplittrim.log || echo "test failed. See r10_readsplittrim.log for details"
# test/dorado_new/test.sh &> r10_readsplittrim.log || echo "test failed. See r10_readsplittrim.log for details"
# unset OPTS_GUPPY
# unset OPTS_EEL
# echo ""
Expand All @@ -113,29 +113,29 @@ echo "********************************************************************"
echo "seqsum"
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
test/dorado/test_seqsum.sh &> seqsum.log || die "test failed. See seqsum.log for details"
test/dorado_new/test_seqsum.sh &> seqsum.log || die "test failed. See seqsum.log for details"
echo ""
echo "********************************************************************"

echo "seqsum - multiple BLOW5"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/blow5/
test/dorado/test_seqsum.sh &> seqsum_multiblow.log
test/dorado_new/test_seqsum.sh &> seqsum_multiblow.log
echo ""
echo "********************************************************************"

echo "demux - FASTQ and SAM"
export PATH_TO_FAST5=/data/slow5-testdata/barcode_test/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test/dorado/test_demux.sh &> demux.log || die "test failed. See demux.log for details"
test/dorado_new/test_demux.sh &> demux.log || die "test failed. See demux.log for details"
echo ""
echo "********************************************************************"

echo "demux - qscore - FASTQ and SAM"
export PATH_TO_FAST5=/data/slow5-testdata/barcode_test/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
test/dorado/test_demux_qscore_split.sh &> demux_qscore.log || die "test failed. See demux_qscore.log for details"
test/dorado_new/test_demux_qscore_split.sh &> demux_qscore.log || die "test failed. See demux_qscore.log for details"
echo ""
echo "********************************************************************"

Expand All @@ -145,7 +145,7 @@ export PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
export OPTS_GUPPY="--trim_adapters "
export OPTS_BARCODER="--enable_trim_barcodes"
export OPTS_EEL=$OPTS_GUPPY" "$OPTS_BARCODER
test/dorado/test_demux_qscore_split.sh &> demux_qscore_trim.log || die "test failed. See demux_qscore_trim.log for details"
test/dorado_new/test_demux_qscore_split.sh &> demux_qscore_trim.log || die "test failed. See demux_qscore_trim.log for details"
unset OPTS_GUPPY
unset OPTS_EEL
echo ""
Expand All @@ -165,7 +165,7 @@ echo "remora"
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_modbases_5mc_cg_fast.cfg
test/dorado/test_remora.sh &> remora.log || die "test failed. See remora.log for details"
test/dorado_new/test_remora.sh &> remora.log || die "test failed. See remora.log for details"
echo ""
echo "********************************************************************"

Expand All @@ -183,7 +183,7 @@ echo "R10.4.1 DNA - FAST model - 500k reads"
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.cfg
test/dorado/test.sh &> dna_500k.log || die "test failed. See dna_500k.log for details"
test/dorado_new/test.sh &> dna_500k.log || die "test failed. See dna_500k.log for details"
echo ""
echo "********************************************************************"

Expand All @@ -193,7 +193,7 @@ export REFIDX=/genome/gencode.v40.transcripts.fa
export PATH_TO_FAST5=/data/hasindu/hasindu2008.git/f5c/test/rna/
export PATH_TO_BLOW5=/data/hasindu/hasindu2008.git/f5c/test/rna/reads.blow5
export MODEL=rna_r9.4.1_70bps_fast.cfg
test/dorado/test.sh &> rna.log || die "test failed. See rna.log for details"
test/dorado_new/test.sh &> rna.log || die "test failed. See rna.log for details"

echo "RNA004 RNA - rna_rp4_130bps_fast"
echo "Not yet implemented :("
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