feat: Sex.DetERRmine

bio/sexdeterrmine/environment.linux-64.pin.txt

@@ -0,0 +1,29 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+# created-by: conda 24.9.2
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda#048b02e3962f066da18efe3a21b77672
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313.conda#381bbd2a92c863f640a55b6ff3c35161
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2024b-hc8b5060_0.conda#8ac3367aafb1cc0a068483c580af8015
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda#cc3573974587f12dda90d96e3e55a702
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda#e39480b9ca41323497b05492a63bc35b
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-hb9d3cd8_0.conda#23cc74f77eb99315c0360ec3533147a9
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
+https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda#aeb98fdeb2e8f25d43ef71fbacbeec80
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.0-hadc24fc_1.conda#b6f02b52a174e612e89548f4663ce56a
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
+https://conda.anaconda.org/conda-forge/linux-64/python-3.13.0-h9ebbce0_100_cp313.conda#08e9aef080f33daeb192b2ddc7e4721f
+https://conda.anaconda.org/conda-forge/noarch/pip-24.3.1-pyh145f28c_0.conda#ca3afe2d7b893a8c8cdf489d30a2b1a3
+https://conda.anaconda.org/bioconda/noarch/sexdeterrmine-1.1.2-hdfd78af_1.tar.bz2#2e9b8e1a34bf366825e78812da25b66a

bio/sexdeterrmine/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - bioconda
+  - conda-forge
+  - nodefaults
+dependencies:
+  - sexdeterrmine=1.1.2

bio/sexdeterrmine/meta.yaml

@@ -0,0 +1,13 @@
+name: Sex.detERRmine
+description: |
+  calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data.
+authors:
+  - Thibault Dayris
+input:
+  - depth: Path to samtools depths file accross multiple samples with a header line giving sample names.
+output:
+  - Path to result table
+params:
+  - No extra parameters handled.
+notes: |
+  See depth header format at: https://github.com/TCLamnidis/Sex.DetERRmine/tree/master?tab=readme-ov-file#instructions

bio/sexdeterrmine/test/Snakefile

@@ -0,0 +1,11 @@
+rule test_sexdeterrmine:
+    input:
+        depth="samples.depth.tsv",
+    output:
+        tsv="results.tsv",
+        json="results.json",
+    threads: 1
+    log:
+        "sexdeterrmine.log",
+    wrapper:
+        "master/bio/sexdeterrmine"

bio/sexdeterrmine/test/samples.depth.tsv

@@ -0,0 +1,5 @@
+#Chr	Pos	Sample1	Sample2	Sample3	Sample4	Sample5
+1	752566	1	1	1	1	1
+X	776546	0	0	0	0	1
+Y	832918	0	1	0	0	0
+Y	842013	0	1	0	3	1

bio/sexdeterrmine/wrapper.py

@@ -0,0 +1,44 @@
+# coding: utf-8
+
+"""Snakemake wrapper for Sex.DetERRmine"""
+
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2024, Thibault Dayris"
+__email__ = "thibault.dayris@gustaveroussy.fr"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+from tempfile import TemporaryDirectory
+
+import os
+import os.path
+
+log = snakemake.log_fmt_shell(
+    stdout=False,
+    stderr=True,
+    append=False,
+)
+extra = snakemake.params.get("extra", "")
+
+with TemporaryDirectory() as tempdir:
+    old_path = os.getcwd()
+    depth_path = os.path.realpath(snakemake.input.depth)
+    os.chdir(tempdir)
+    shell(f"sexdeterrmine --Input {depth_path} {extra} > out.tsv 2> sexdeterrmine.log")
+
+    log = snakemake.log_fmt_shell(
+        stdout=True,
+        stderr=True,
+        append=True,
+    )
+
+    os.chdir(old_path)
+    os.replace(f"{tempdir}/sexdeterrmine.log", str(snakemake.log))
+
+    tsv = snakemake.output.get("tsv")
+    if tsv:
+        shell("mv --verbose {tempdir}/out.tsv {tsv} {log}")
+
+    json = snakemake.output.get("json")
+    if json:
+        shell("mv --verbose {tempdir}/sexdeterrmine.json {json} {log}")

test_wrappers.py

@@ -4615,6 +4615,12 @@ def test_gseapy_gsea(run):
     )
 
 
+def test_sexdeterrmine(run):
+    run(
+        "bio/sexdeterrmine",
+        ["snakemake", "--cores", "1", "results.tsv", "-F", "--use-conda"],
+    )
+
 def test_sourmash_compute(run):
     run(
         "bio/sourmash/compute/",