Merge branch 'dev' into meth

hasindu2008 · Jul 17, 2024 · d7a3784 · d7a3784
2 parents be9e20d + 4241f69
commit d7a3784
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Showing 10 changed files with 146 additions and 2 deletions.
diff --git a/scripts/test.sh b/scripts/test.sh
@@ -21,15 +21,18 @@ ex() {
     fi
 }
 
+# DNA R9
 echo "Basic DNA"
 ex ./squigulator test/nCoV-2019.reference.fasta -o a.slow5 -q a.fasta -n 10 --seed 1 --dwell-std 1.0 -r 20000 -t1 || die "Running the tool failed"
 diff -q test/fasta.exp a.fasta || die "diff failed"
 diff -q test/slow5.exp a.slow5 || die "diff failed"
 
+# RNA R9
 echo "Basic RNA"
 ex ./squigulator -x rna-r9-prom test/rnasequin_sequences_2.4.fa -o a.slow5 -q a.fastq -n 10 --seed 1 --prefix=yes --dwell-std 3.0 -t1  || die "Running the tool failed"
 diff -q test/rna_slow5.exp a.slow5 || die "diff failed"
 
+# --ideal
 echo "--ideal"
 ex ./squigulator test/nCoV-2019.reference.fasta -o a.slow5 -n 2 --seed 1 --ideal  -r 20000 -t1 || die "Running the tool failed"
 diff -q test/dna_ideal_slow5.exp a.slow5 || die "diff failed"
@@ -44,25 +47,31 @@ diff -q test/dna_ideal_amp_slow5.exp a.slow5 || die "diff failed"
 ex ./squigulator test/nCoV-2019.reference.fasta -o a.slow5 -n 2 --seed 1 --amp-noise 0.0  -r 20000  --dwell-std 5.0 -t1 || die "Running the tool failed"
 diff -q test/dna_ideal_amp_slow5.exp a.slow5 || die "diff failed"
 
-
+# prefixes for dna
 echo "--prefix=yes"
 ex ./squigulator test/nCoV-2019.reference.fasta -o a.slow5 -n 2 --seed 1 --prefix=yes  -r 20000  --dwell-std 5.0 -t1 || die "Running the tool failed"
 diff -q test/dna_prefix_slow5.exp a.slow5 || die "diff failed"
 
+# prefixes for rnana
+
 echo "--prefix=no"
 ex ./squigulator -x rna-r9-prom test/rnasequin_sequences_2.4.fa -o a.slow5 -n 2 --seed 1 --dwell-std 3.0 -t1 || die "Running the tool failed"
 diff -q test/rna_prefixno_slow5.exp a.slow5 || die "diff failed"
 
+
+# full contigs
 echo "--full-contigs"
 ex ./squigulator test/nCoV-2019.reference.fasta -o a.slow5 --seed 1 --full-contigs  --dwell-std 5.0 -t1 || die "Running the tool failed"
 diff -q test/dna_full_contig.exp a.slow5 || die "diff failed"
 
+# r10 and paf and fasta
 echo "r10 PAF out"
 ex ./squigulator -x dna-r10-prom -o a.slow5 -n 1 --seed 1 --dwell-std 4.0 -t1 test/nCoV-2019.reference.fasta -c a.paf -q a.fa
 diff -q test/dna_r10_paf.exp a.slow5 || die "diff failed"
 diff -q test/dna_r10_paf.paf.exp a.paf || die "diff failed"
 diff -q test/dna_r10_paf.fa.exp a.fa || die "diff failed"
 
+# r9 rna paf and sam and fasta outputs
 echo "r9 rna paf out and sam out"
 ex ./squigulator -x rna-r9-prom -o a.slow5 -n 1 --seed 1 --dwell-std 3.0 -t1 -t1 test/rnasequin_sequences_2.4.fa -c a.paf -q a.fa -a a.sam
 diff -q test/rna_paf.exp a.slow5 || die "diff failed"
@@ -82,7 +91,43 @@ ex ./squigulator -x dna-r10-prom -o a.slow5 -n 2 --seed 2 --dwell-std 4.0 -t1 te
 diff -q test/dna_r10_paf-ref.exp a.slow5 || die "diff failed"
 diff -q test/dna_r10_paf-ref.sam.exp a.sam || die "diff failed"
 
+# rna004
+echo "rna004 test"
+ex ./squigulator -x rna004-prom -o a.slow5 -n 1 --seed 1 --dwell-std 3.0 -t1 test/rnasequin_sequences_2.4.fa
+diff -q test/rna004.slow5.exp a.slow5 || die "diff failed"
+
+# -r and -f and --amp-noise
+echo "read lens and fold coverage"
+ex ./squigulator -x dna-r10-prom -o a.slow5 -r 20000 -f 1 --seed 2 --amp-noise 0.5 -t1 test/nCoV-2019.reference.fasta
+diff -q test/dna_r10_amp_noise.exp a.slow5 || die "diff failed"
+
+# dwell mean and std
+ex ./squigulator -x rna004-min -o a.slow5 -n 1 --seed 1 --dwell-mean 30 --dwell-std 3.0 -t1 test/rnasequin_sequences_2.4.fa
+diff -q test/rna004_dwell.exp a.slow5 || die "diff failed"
+
+# bps
+ex ./squigulator -x dna-r10-prom -o a.slow5 --seed 1 --bps 200 -t1 -n 2 test/nCoV-2019.reference.fasta
+diff -q test/bps.exp a.slow5  || die "diff failed"
+
+# cdna
+ex ./squigulator -x dna-r10-min -o a.slow5 -n 1 --seed 1 --dwell-std 3.0 -t1 test/rnasequin_sequences_2.4.fa --cdna
+diff -q test/cdna.exp a.slow5 || die "diff failed"
+
+# trans count
+
+# trans trunc
+ex ./squigulator -x rna004-prom -o a.slow5 -n 1 --seed 1 --trans-trunc -t1 test/rnasequin_sequences_2.4.fa
+diff -q test/trans_trunc.exp a.slow5 || die "diff failed"
+
+# ont-friendly
+ex ./squigulator -x dna-r10-min -o a.slow5 -n 1 --seed 1 -t1 test/rnasequin_sequences_2.4.fa --ont-friendly=yes
+diff -q test/ont_friendly.exp a.slow5 || die "diff failed"
+
+# digitisation, sample-rate, range, offset-mean, offset-std, median-before-mean, median-before-std
+ex ./squigulator -x dna-r10-min -o a.slow5 -n 1 --seed 1 -t1 test/rnasequin_sequences_2.4.fa --digitisation 4096 --sample-rate 10000 --range 300 --offset-mean -1000 --offset-std 0 --median-before-mean 100 --median-before-std 0
+diff -q test/dev.exp a.slow5 || die "diff failed"
 
+# threads and batch size
 redundancy_check () {
     N=$(grep -v ^[@#] a.slow5 | cut -f ${1}  | sort | uniq -c | sort -nr -k1,1 | head -1 | awk '{print $1}')
     [ "$N" != "1" ] && die "failed thread test for column ${1}"

diff --git a/test/bps.exp b/test/bps.exp
diff --git a/test/cdna.exp b/test/cdna.exp
diff --git a/test/dev.exp b/test/dev.exp
diff --git a/test/dna_r10_amp_noise.exp b/test/dna_r10_amp_noise.exp
diff --git a/test/ont_friendly.exp b/test/ont_friendly.exp
diff --git a/test/rna004.slow5.exp b/test/rna004.slow5.exp
diff --git a/test/rna004_dwell.exp b/test/rna004_dwell.exp
diff --git a/test/test_extensive.sh b/test/test_extensive.sh
@@ -82,4 +82,6 @@ echo "RNA004 RNA"
 identityrna.sh $REF_GENCODE new.fastq > a.acc 2>> a.log || die "identitydna failed"
 cat a.acc
 CHECK_ACC 0.77 a.acc
-REMOVE_TMP
+REMOVE_TMP
+
+# CDNA
diff --git a/test/trans_trunc.exp b/test/trans_trunc.exp