Skip to content

Commit

Permalink
tests: test_cmdline: Use minimap2 as standard for osx action.
Browse files Browse the repository at this point in the history
  • Loading branch information
@wwood
wwood committed Sep 17, 2024
1 parent f62adf7 commit 57037eb
Showing 1 changed file with 75 additions and 27 deletions.
102 changes: 75 additions & 27 deletions tests/test_cmdline.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,8 @@ mod tests {
"-2",
"tests/data/reads_for_seq1_and_seq2.2.fq.gz",
"--proper-pairs-only",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -227,6 +229,8 @@ mod tests {
"--proper-pairs-only",
"--output-format",
"sparse",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -277,6 +281,8 @@ mod tests {
"tests/data/7seqs.fna",
"-s",
"~",
"-p",
"minimap2-sr",
])
.succeeds()
.unwrap();
Expand All @@ -292,6 +298,8 @@ mod tests {
"tests/data/reads_for_seq1_and_seq2.2.fq.gz",
"--reference",
"tests/data/7seqs.fna",
"-p",
"minimap2-sr",
])
.succeeds()
.unwrap();
Expand All @@ -310,6 +318,8 @@ mod tests {
"sparse",
"--reference",
"tests/data/7seqs.fna",
"-p",
"minimap2-sr",
"--bam-file-cache-directory",
td.path().to_str().unwrap(),
])
Expand Down Expand Up @@ -366,28 +376,6 @@ mod tests {
.unwrap();
}

#[test]
fn test_make() {
let td = tempfile::TempDir::new().unwrap();
Assert::main_binary()
.with_args(&[
"make",
"--coupled",
"tests/data/reads_for_seq1_and_seq2.1.fq.gz",
"tests/data/reads_for_seq1_and_seq2.2.fq.gz",
"--reference",
"tests/data/7seqs.fna",
"--output-directory",
td.path().to_str().unwrap(),
])
.succeeds()
.unwrap();
assert!(td
.path()
.join("7seqs.fna.reads_for_seq1_and_seq2.1.fq.gz.bam")
.is_file());
}

#[test]
fn test_make_with_mkdir() {
let td = tempfile::TempDir::new().unwrap();
Expand All @@ -401,6 +389,8 @@ mod tests {
"tests/data/7seqs.fna",
"--output-directory",
format!("{}/unmade_directory", td.path().to_str().unwrap()).as_str(),
"-p",
"minimap2-sr",
])
.succeeds()
.unwrap();
Expand All @@ -425,6 +415,8 @@ mod tests {
"tests/data/7seqs.fna",
"-s",
"~",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -545,6 +537,8 @@ genome6 0",
"tests/data/reads_for_seq1_and_seq2.fna",
"-s",
"~",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -586,6 +580,8 @@ genome6 0",
"tests/data/reads_for_seq1_and_seq2.2.fq.gz",
"--single",
"tests/data/reads_for_seq1_and_seq2.fna",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -831,6 +827,8 @@ k141_109815 362 0.6274 0.6274 0.2349").unwrap();
"0.01",
"--trim-min",
"0.009",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -865,6 +863,8 @@ k141_109815 362 0.6274 0.6274 0.2349").unwrap();
"0.01",
"--trim-min",
"0.009",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -897,6 +897,8 @@ k141_109815 362 0.6274 0.6274 0.2349").unwrap();
"0.01",
"--trim-min",
"0.009",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -930,6 +932,8 @@ reads_for_seq1_and_seq2.1.fq.gz seq2 0 1.2435294 0.849",
"0.01",
"--trim-min",
"0.009",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -959,6 +963,8 @@ reads_for_seq1_and_seq2.1.fq.gz seq2 0 1.2435294 0.849",
"0.01",
"--trim-min",
"0.009",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand All @@ -982,6 +988,8 @@ reads_for_seq1_and_seq2.1.fq.gz seq2 0 1.2435294 0.849",
"tests/data/dense_interleaved_single_genome_bug/reads_interleaved2.fna",
"--output-format",
"dense",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -1104,6 +1112,8 @@ reads_for_seq1_and_seq2.1.fq.gz seq2 0 1.2435294 0.849",
"tests/data/genomes_dir/",
"-x",
".fna",
"-p",
"minimap2-sr",
])
.succeeds()
.unwrap();
Expand All @@ -1120,6 +1130,8 @@ reads_for_seq1_and_seq2.1.fq.gz seq2 0 1.2435294 0.849",
"tests/data/reads_for_seq1_and_seq2.2.fq.gz",
"--genome-fasta-directory",
"tests/data/genomes_dir/",
"-p",
"minimap2-sr",
"--bam-file-cache-directory",
td.path().to_str().unwrap(),
])
Expand Down Expand Up @@ -1287,6 +1299,8 @@ genome6 26.697144
"--proper-pairs-only",
"--min-read-aligned-length-pair",
"50",
"-p",
"minimap2-sr",
])
.stderr()
.contains(
Expand All @@ -1309,6 +1323,8 @@ genome6 26.697144
"tests/data/7seqs.fna",
"--min-read-aligned-length",
"50",
"-p",
"minimap2-sr",
])
.stderr()
.contains(
Expand All @@ -1320,7 +1336,7 @@ genome6 26.697144
}

#[test]
fn test_sharded_contig_input_reads() {
fn test_sharded_contig_input_reads_strobealign() {
Assert::main_binary()
.with_args(&[
"contig",
Expand Down Expand Up @@ -1408,6 +1424,8 @@ genome6 26.697144
"tests/data/7seqs.fna",
"--interleaved",
"tests/data/reads_for_seq1_and_seq2.fna",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand All @@ -1434,6 +1452,8 @@ genome6 26.697144
"-2",
"tests/data/7seqs.reads_for_7.2.fq",
"tests/data/random.fq",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -1944,6 +1964,8 @@ genome6~random_sequence_length_11003 0 0 0
"--dereplicate",
"--single",
"tests/data/set1/1read.actually_fasta.fq",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -1986,6 +2008,8 @@ genome6~random_sequence_length_11003 0 0 0
td_copy.path().to_str().unwrap(),
"--dereplication-output-representative-list",
t_reps,
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -2046,6 +2070,8 @@ genome6~random_sequence_length_11003 0 0 0
"--dereplicate",
"--single",
"tests/data/set1/1read.actually_fasta.fq",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand All @@ -2071,6 +2097,8 @@ genome6~random_sequence_length_11003 0 0 0
"tests/data/set1/checkm.tsv",
"--single",
"tests/data/set1/1read.actually_fasta.fq",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand All @@ -2097,6 +2125,8 @@ genome6~random_sequence_length_11003 0 0 0
"--dereplicate",
"--single",
"tests/data/set1/1read.actually_fasta.fq",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand All @@ -2122,6 +2152,8 @@ genome6~random_sequence_length_11003 0 0 0
"tests/data/set1/genomeInfo.csv",
"--single",
"tests/data/set1/1read.actually_fasta.fq",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -2152,6 +2184,8 @@ genome6~random_sequence_length_11003 0 0 0
"0",
"--single",
"tests/data/set1/1read.actually_fasta.fq",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -2236,14 +2270,16 @@ genome6~random_sequence_length_11003 0 0 0
"--min-covered-fraction",
"0.05",
"--exclude-supplementary",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
.satisfies(
|observed| {
assert_equal_table(
"Genome 20120700_S3D.head100000.1.fq.gz Mean 20120700_S3D.head100000.1.fq.gz Covered Fraction\n\
73.20120700_S3D.10\t0.06966771\t0.06644242\n73.20120700_S3D.12\t0\t0\n73.20120700_S3D.15\t0\t0\n73.20120700_S3D.16\t0\t0\n73.20120700_S3D.34\t0.056637306\t0.054271795\n73.20120700_S3D.3\t0\t0\n73.20120700_S3D.5\t0.13356309\t0.12263384\n73.20120700_S3D.7\t0.097519465\t0.09129343\n\
73.20120700_S3D.10\t0.071023874\t0.06777273\n73.20120700_S3D.12\t0\t0\n73.20120700_S3D.15\t0\t0\n73.20120700_S3D.16\t0\t0\n73.20120700_S3D.34\t0.06653676\t0.0630154\n73.20120700_S3D.3\t0\t0\n73.20120700_S3D.5\t0.1341526\t0.123165175\n73.20120700_S3D.7\t0.100108385\t0.093486056\n\
",
observed,
)
Expand Down Expand Up @@ -2432,7 +2468,7 @@ genome6~random_sequence_length_11003 0 0 0
}

#[test]
fn test_contig_output_file() {
fn test_contig_output_file_strobealign() {
let tf: tempfile::NamedTempFile = tempfile::NamedTempFile::new().unwrap();
let t = tf.path().to_str().unwrap();

Expand Down Expand Up @@ -2511,6 +2547,8 @@ genome6~random_sequence_length_11003 0 0 0
"--coupled",
"tests/data/contig_name_clashing/reads_for_genome2.1.fa",
"tests/data/contig_name_clashing/reads_for_genome2.2.fa",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -2538,6 +2576,8 @@ genome6~random_sequence_length_11003 0 0 0
"--coupled",
"tests/data/contig_name_clashing/reads_for_genome2.1.fa",
"tests/data/contig_name_clashing/reads_for_genome2.2.fa",
"-p",
"minimap2-sr",
])
.fails()
.stderr()
Expand Down Expand Up @@ -2698,7 +2738,7 @@ genome6~random_sequence_length_11003 0 0 0
}

#[test]
fn test_genomes_and_contigs_with_supplementary() {
fn test_genomes_and_contigs_with_supplementary_strobealign() {
Assert::main_binary()
.with_args(&[
"genome",
Expand Down Expand Up @@ -2820,7 +2860,9 @@ genome6~random_sequence_length_11003 0 0 0
"tests/data/rhys_bug/20120700_S3D.stray_read1.2.fq",
"--min-covered-fraction",
"0",
"--exclude-supplementary"
"--exclude-supplementary",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -2905,6 +2947,8 @@ genome6~random_sequence_length_11003 0 0 0
"--min-covered-fraction",
"0",
"--exclude-supplementary",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -2958,6 +3002,8 @@ genome6~random_sequence_length_11003 0 0 0
"-2",
"tests/data/reads_for_seq1_and_seq2.2.fq.gz",
"--proper-pairs-only",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down Expand Up @@ -3000,6 +3046,8 @@ genome6~random_sequence_length_11003 0 0 0
"-m",
"mean",
"covered_fraction",
"-p",
"minimap2-sr",
])
.succeeds()
.stdout()
Expand Down

0 comments on commit 57037eb

Please sign in to comment.