diff --git a/bio/nonpareil/infer/environment.linux-64.pin.txt b/bio/nonpareil/infer/environment.linux-64.pin.txt index 25e146393c6..8fc565e1d3e 100644 --- a/bio/nonpareil/infer/environment.linux-64.pin.txt +++ b/bio/nonpareil/infer/environment.linux-64.pin.txt @@ -1,105 +1,104 @@ # This file may be used to create an environment using: # $ conda create --name --file # platform: linux-64 -# created-by: conda 24.9.2 +# created-by: conda 25.9.1 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 -https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda#f0991f0f84902f6b6009b4d2350a83aa https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_8.conda#ff007ab0f0fdc53d245972bba8a6d40c -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 -https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-15.1.0-h4c094af_105.conda#a38922dbdf037d78b3d00d6d0a0399da -https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 -https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-15.1.0-h4c094af_105.conda#3bc809fa9c4b2cd49ed38fe555af5f99 -https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-8_cp313.conda#94305520c52a4aa3f6c2b1ff6008d9f8 +https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-15.2.0-h73f6952_107.conda#85fce551e54a1e81b69f9ffb3ade6aee +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe +https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-15.2.0-h73f6952_107.conda#a888a479d58f814ee9355524cc94edf3 +https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda#0539938c55b6b1a59b560e843ad864a4 https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d 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The kmer kernel implements an error correction function only compatible with FastQ + [ 0.0] Reading reads/a.fa + [ 0.0] Picking 11 random sequences + [ 0.0] Counting Kmers + [ 0.0] Read file with 15 sequences + [ 0.0] Average read length is 7.000000bp + [ 0.0] Sub-sampling library + [ 0.0] Sampling at 0.000000% + [ 0.0] Sampling at 11.764900% + [ 0.0] Sampling at 16.807000% + [ 0.0] Sampling at 24.010000% + [ 0.0] Sampling at 34.300000% + [ 0.0] Sampling at 49.000000% + [ 0.0] Sampling at 70.000000% + [ 0.0] Sampling at 100.000000% + [ 0.0] Evaluating consistency + [ 0.0] The coverage of this dataset is very high, and the precise value might be slighly off + [ 0.0] Not to be worried, this simply means that your dataset is too good to need heuristic estimates! + [ 0.0] WARNING: The curve reached near-saturation in 6 or fewer points, hence diversity estimations could be unreliable + [ 0.0] To increase the resolution of the curve increase -d, currently set at 0.700000 diff --git a/bio/nonpareil/infer/test/expected/a.fa.npc b/bio/nonpareil/infer/test/expected/a.fa.npc new file mode 100644 index 00000000000..c06aca8419e --- /dev/null +++ b/bio/nonpareil/infer/test/expected/a.fa.npc @@ -0,0 +1,11 @@ +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 diff --git a/bio/nonpareil/infer/test/expected/a.fas.bz2.npc b/bio/nonpareil/infer/test/expected/a.fas.bz2.npc new file mode 100644 index 00000000000..c06aca8419e --- /dev/null +++ b/bio/nonpareil/infer/test/expected/a.fas.bz2.npc @@ -0,0 +1,11 @@ +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 diff --git a/bio/nonpareil/infer/test/expected/a.fasta.gz.npc b/bio/nonpareil/infer/test/expected/a.fasta.gz.npc new file mode 100644 index 00000000000..c06aca8419e --- /dev/null +++ b/bio/nonpareil/infer/test/expected/a.fasta.gz.npc @@ -0,0 +1,11 @@ +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 diff --git a/bio/nonpareil/infer/test/expected/a.fastq.gz.npc b/bio/nonpareil/infer/test/expected/a.fastq.gz.npc new file mode 100644 index 00000000000..c06aca8419e --- /dev/null +++ b/bio/nonpareil/infer/test/expected/a.fastq.gz.npc @@ -0,0 +1,11 @@ +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 diff --git a/bio/nonpareil/infer/test/expected/a.fq.bz2.npc b/bio/nonpareil/infer/test/expected/a.fq.bz2.npc new file mode 100644 index 00000000000..c06aca8419e --- /dev/null +++ b/bio/nonpareil/infer/test/expected/a.fq.bz2.npc @@ -0,0 +1,11 @@ +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 diff --git a/bio/nonpareil/infer/test/expected/a.fq.log b/bio/nonpareil/infer/test/expected/a.fq.log new file mode 100644 index 00000000000..78de2ad6add --- /dev/null +++ b/bio/nonpareil/infer/test/expected/a.fq.log @@ -0,0 +1,20 @@ + [ 0.0] Reducing query reads (-X) to 11 + [ 0.0] Reading reads/a.fq + [ 0.0] Picking 11 random sequences + [ 0.0] Counting kmers + [ 0.0] Read file with 15 sequences + [ 0.0] Average read length is 7.000000bp + [ 0.0] Sub-sampling library + [ 0.0] Sampling at 0.000000% + [ 0.0] Sampling at 11.764900% + [ 0.0] Sampling at 16.807000% + [ 0.0] Sampling at 24.010000% + [ 0.0] Sampling at 34.300000% + [ 0.0] Sampling at 49.000000% + [ 0.0] Sampling at 70.000000% + [ 0.0] Sampling at 100.000000% + [ 0.0] Evaluating consistency + [ 0.0] The coverage of this dataset is very high, and the precise value might be slighly off + [ 0.0] Not to be worried, this simply means that your dataset is too good to need heuristic estimates! + [ 0.0] WARNING: The curve reached near-saturation in 6 or fewer points, hence diversity estimations could be unreliable + [ 0.0] To increase the resolution of the curve increase -d, currently set at 0.700000 diff --git a/bio/nonpareil/infer/test/expected/a.fq.npc b/bio/nonpareil/infer/test/expected/a.fq.npc new file mode 100644 index 00000000000..c06aca8419e --- /dev/null +++ b/bio/nonpareil/infer/test/expected/a.fq.npc @@ -0,0 +1,11 @@ +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 diff --git a/bio/nonpareil/infer/test/expected/empty.fq.bz2.npa 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b/bio/nonpareil/infer/test/expected/empty.fq.bz2.npc new file mode 100644 index 00000000000..e69de29bb2d diff --git a/bio/nonpareil/infer/test/expected/empty.fq.bz2.npo b/bio/nonpareil/infer/test/expected/empty.fq.bz2.npo new file mode 100644 index 00000000000..83301f7f107 --- /dev/null +++ b/bio/nonpareil/infer/test/expected/empty.fq.bz2.npo @@ -0,0 +1,10 @@ +# @impl: Nonpareil +# @ksize: 3 +# @version: 3.5.5 +# @L: 100.000 +# @AL: 98.000 +# @R: 1 +# @overlap: 50.00 +# @divide: 0.70 +0.000000 0.00000 0.00000 0.00000 0.00000 0.00000 +0.000000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/bio/nonpareil/infer/test/expected/empty.fq.gz.npa b/bio/nonpareil/infer/test/expected/empty.fq.gz.npa new file mode 100644 index 00000000000..948641aac8a --- /dev/null +++ b/bio/nonpareil/infer/test/expected/empty.fq.gz.npa @@ -0,0 +1,1024 @@ +0.00 0 0.0000000000 +0.00 1 0.0000000000 +0.00 2 0.0000000000 +0.00 3 0.0000000000 +0.00 4 0.0000000000 +0.00 5 0.0000000000 +0.00 6 0.0000000000 +0.00 7 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+0.00 1020 0.0000000000 +0.00 1021 0.0000000000 +0.00 1022 0.0000000000 +0.00 1023 0.0000000000 diff --git a/bio/nonpareil/infer/test/expected/empty.fq.npc b/bio/nonpareil/infer/test/expected/empty.fq.npc new file mode 100644 index 00000000000..e69de29bb2d diff --git a/bio/nonpareil/infer/test/expected/empty.fq.npo b/bio/nonpareil/infer/test/expected/empty.fq.npo new file mode 100644 index 00000000000..83301f7f107 --- /dev/null +++ b/bio/nonpareil/infer/test/expected/empty.fq.npo @@ -0,0 +1,10 @@ +# @impl: Nonpareil +# @ksize: 3 +# @version: 3.5.5 +# @L: 100.000 +# @AL: 98.000 +# @R: 1 +# @overlap: 50.00 +# @divide: 0.70 +0.000000 0.00000 0.00000 0.00000 0.00000 0.00000 +0.000000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/bio/nonpareil/infer/test/reads/empty.fq b/bio/nonpareil/infer/test/reads/empty.fq new file mode 100644 index 00000000000..e69de29bb2d diff --git a/bio/nonpareil/infer/test/reads/empty.fq.bz2 b/bio/nonpareil/infer/test/reads/empty.fq.bz2 new file mode 100644 index 00000000000..b56f3b974d6 Binary files /dev/null and b/bio/nonpareil/infer/test/reads/empty.fq.bz2 differ diff --git a/bio/nonpareil/infer/test/reads/empty.fq.gz b/bio/nonpareil/infer/test/reads/empty.fq.gz new file mode 100644 index 00000000000..9736d08d781 Binary files /dev/null and b/bio/nonpareil/infer/test/reads/empty.fq.gz differ diff --git a/bio/nonpareil/infer/wrapper.py b/bio/nonpareil/infer/wrapper.py index b1763901551..06157416a5d 100644 --- a/bio/nonpareil/infer/wrapper.py +++ b/bio/nonpareil/infer/wrapper.py @@ -2,33 +2,18 @@ __copyright__ = "Copyright 2023, Filipe G. Vieira" __license__ = "MIT" -from os import path import tempfile +from pathlib import Path from snakemake.shell import shell -from snakemake_wrapper_utils.snakemake import get_mem +from snakemake_wrapper_utils.snakemake import get_mem, get_format log = snakemake.log_fmt_shell(stdout=True, stderr=True) extra = snakemake.params.get("extra", "") mem_mb = get_mem(snakemake, out_unit="MiB") -uncomp = "" -in_name, in_ext = path.splitext(snakemake.input[0]) -if in_ext in [".gz", ".bz2"]: - uncomp = ( - f"pbzip2 -p{snakemake.threads} --decompress --stdout" - if in_ext == ".bz2" - else "" - ) - in_name, in_ext = path.splitext(in_name) - # Infer output format -if in_ext in [".fa", ".fas", ".fasta"]: - in_format = "fasta" -elif in_ext in [".fq", ".fastq"]: - in_format = "fastq" -else: - raise ValueError("invalid input format") +in_format = get_format(snakemake.input[0]) # Redundancy summary redund_sum = snakemake.output.get("redund_sum", "") @@ -52,12 +37,36 @@ with tempfile.NamedTemporaryFile() as tmp: - if uncomp: + # Uncompress bzip2 input files + if Path(snakemake.input[0]).suffix == ".bz2": in_uncomp = tmp.name - shell("{uncomp} {snakemake.input[0]} > {tmp.name}") + shell( + "pbzip2 -p{snakemake.threads} --decompress --stdout {snakemake.input[0]} > {tmp.name}" + ) else: in_uncomp = snakemake.input[0] + # Check if input file is empty + empty = Path(in_uncomp).stat().st_size == 0 + if Path(in_uncomp).suffix == ".gz" and Path(in_uncomp).stat().st_size < 50: + import gzip + + with gzip.open(in_uncomp, "rt") as f: + empty = not bool(f.readlines()) + + # If empty, provide dummy input file so that program does not crash + # https://github.com/lmrodriguezr/nonpareil/issues/71 + if empty: + in_uncomp = tmp.name + with open(in_uncomp, "wt") as f: + if in_format == "fasta": + f.write("\n".join([">dummy1", "N" * 100])) + elif in_format == "fastq": + f.write("\n".join(["@dummy1", "N" * 100, "+", "!" * 100])) + else: + raise ValueError(f"invalid format: {in_format}") + f.write("\n") + shell( "nonpareil" " -t {snakemake.threads}" @@ -68,3 +77,7 @@ " {extra}" " {log}" ) + + if empty and redund_sum: + with open(redund_sum, "at") as f: + f.write("\t".join(["0.000000"] + ["0.00000"] * 5) + "\n") diff --git a/bio/nonpareil/plot/test/Snakefile b/bio/nonpareil/plot/test/Snakefile index 2ce3defc0b5..bdebdf7af84 100644 --- a/bio/nonpareil/plot/test/Snakefile +++ b/bio/nonpareil/plot/test/Snakefile @@ -16,7 +16,7 @@ rule test_nonpareil_plot: use rule test_nonpareil_plot as test_nonpareil_plot_multiple with: input: - npo=["a.npo", "b.npo", "c.npo"], + npo=["a.npo", "b.npo", "c.npo", "d.npo"], output: pdf="results/samples.pdf", tsv="results/samples.tsv", @@ -24,7 +24,7 @@ use rule test_nonpareil_plot as test_nonpareil_plot_multiple with: log: "logs/samples.log", params: - extra="--labels 'Model A,Model B,Model C' --col blue,red,green", + extra="--labels 'Model A,Model B,Model C,Model D' --col blue,red,green,yellow", use rule test_nonpareil_plot as test_nonpareil_plot_nomodel with: diff --git a/bio/nonpareil/plot/test/d.npo b/bio/nonpareil/plot/test/d.npo new file mode 100644 index 00000000000..a799f7e80e4 --- /dev/null +++ b/bio/nonpareil/plot/test/d.npo @@ -0,0 +1,10 @@ +# @impl: Nonpareil +# @ksize: 3 +# @version: 3.5.5 +# @L: 100.000 +# @AL: 98.000 +# @R: 1 +# @overlap: 50.00 +# @divide: 0.70 +0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/bio/nonpareil/plot/wrapper.py b/bio/nonpareil/plot/wrapper.py index 14debb7190f..4b2271b15a6 100644 --- a/bio/nonpareil/plot/wrapper.py +++ b/bio/nonpareil/plot/wrapper.py @@ -3,6 +3,7 @@ __license__ = "MIT" +import tempfile from pathlib import Path from snakemake.shell import shell @@ -10,10 +11,28 @@ log = snakemake.log_fmt_shell(stdout=True, stderr=True) -for output in snakemake.output: - ext = Path(output).suffix.lstrip(".") - if ext in ["json", "tsv", "pdf"]: - extra += f" --{ext} {output}" +with tempfile.NamedTemporaryFile() as tmp: + for output in snakemake.output: + ext = Path(output).suffix.lstrip(".") + if ext in ["json", "tsv", "pdf"]: + if ext == "json": + extra += f" --{ext} {tmp.name}" + else: + extra += f" --{ext} {output}" -shell("NonpareilCurves.R {extra} {snakemake.input} {log}") + shell("NonpareilCurves.R {extra} {snakemake.input} {log}") + + # Fix JSON output file + # https://github.com/lmrodriguezr/nonpareil/issues/70 + json_out = snakemake.output.get("json") + if json_out: + import json + import numpy as np + + with open(tmp.name, "rt") as json_f: + json_data = json.load(json_f) + for key, val in json_data.items(): + val["x.adj"] = [np.nan if x == "NaN" else x for x in val["x.adj"]] + with open(json_out, "wt") as json_f: + json.dump(json_data, json_f, indent=4) diff --git a/test_wrappers.py b/test_wrappers.py index 6cfc1eec8cc..6fd9a14e41a 100644 --- a/test_wrappers.py +++ b/test_wrappers.py @@ -107,7 +107,6 @@ def _run(wrapper, cmd, check_log=None, compare_results_with_expected=None): f"file://{tmp_test_subdir}/", ] - if CONTAINERIZED: # run snakemake in container cmd = [ @@ -129,9 +128,7 @@ def _run(wrapper, cmd, check_log=None, compare_results_with_expected=None): with open(generated) as genf, open(expected) as expf: gen_lines = genf.readlines() exp_lines = expf.readlines() - diff = "".join( - difflib.Differ().compare(gen_lines, exp_lines) - ) + diff = "".join(difflib.Differ().compare(gen_lines, exp_lines)) raise ValueError( f"Unexpected results: {generated} != {expected}." f"Diff:\n{diff}" @@ -271,9 +268,19 @@ def test_agat(run): def test_alignoth(run): run( "bio/alignoth", - ["snakemake", "--cores", "1", "--use-conda", "-F", "out/json_plot.vl.json", "out/plot.html", "output-dir/"], + [ + "snakemake", + "--cores", + "1", + "--use-conda", + "-F", + "out/json_plot.vl.json", + "out/plot.html", + "output-dir/", + ], ) + def test_alignoth_report_meta(run): run( "meta/bio/alignoth_report", @@ -383,40 +390,64 @@ def test_nonpareil(run): "results/a.fq.npo", "results/a.fq.bz2.npo", "results/a.fastq.gz.npo", + "results/empty.fq.bz2.npo", + "results/empty.fq.gz.npo", + "results/empty.fq.npo", ], + compare_results_with_expected={ + "results/a.fa.log": "expected/a.fa.log", + "results/a.fa.npc": "expected/a.fa.npc", + "results/a.fas.bz2.npc": "expected/a.fas.bz2.npc", + "results/a.fasta.gz.npc": "expected/a.fasta.gz.npc", + "results/a.fq.log": "expected/a.fq.log", + "results/a.fq.npc": "expected/a.fq.npc", + "results/a.fq.bz2.npc": "expected/a.fq.bz2.npc", + "results/a.fastq.gz.npc": "expected/a.fastq.gz.npc", + "results/empty.fq.bz2.npa": "expected/empty.fq.bz2.npa", + "results/empty.fq.bz2.npc": "expected/empty.fq.bz2.npc", + "results/empty.fq.bz2.npo": "expected/empty.fq.bz2.npo", + "results/empty.fq.gz.npa": "expected/empty.fq.gz.npa", + "results/empty.fq.gz.npc": "expected/empty.fq.gz.npc", + "results/empty.fq.gz.npo": "expected/empty.fq.gz.npo", + "results/empty.fq.npa": "expected/empty.fq.npa", + "results/empty.fq.npc": "expected/empty.fq.npc", + "results/empty.fq.npo": "expected/empty.fq.npo", + }, ) -def test_ngsbits_samplesimilarity(run): +def test_nonpareil_plot(run): run( - "bio/ngsbits/samplesimilarity", + "bio/nonpareil/plot", [ "snakemake", "--cores", "1", "--use-conda", "-F", - "similarity.tsv", + "results/a.pdf", + "results/b.pdf", + "results/c.pdf", + "results/d.pdf", + "results/a.nomodel.pdf", + "results/b.nomodel.pdf", + "results/c.nomodel.pdf", + "results/d.nomodel.pdf", + "results/samples.pdf", ], ) -def test_nonpareil_plot(run): +def test_ngsbits_samplesimilarity(run): run( - "bio/nonpareil/plot", + "bio/ngsbits/samplesimilarity", [ "snakemake", "--cores", "1", "--use-conda", "-F", - "results/a.pdf", - "results/b.pdf", - "results/c.pdf", - "results/a.nomodel.pdf", - "results/b.nomodel.pdf", - "results/c.nomodel.pdf", - "results/samples.pdf", + "similarity.tsv", ], ) @@ -7152,7 +7183,7 @@ def test_orthanq(run): "--use-conda", "out/candidates", "out/candidates.vcf", -# "out/preprocess_hla.bcf", + # "out/preprocess_hla.bcf", "out/preprocess_virus.bcf", "out/calls_hla", "out/calls_virus",