feat: Bustools count (#511)

* [fix] (template): Missing code in wrappers' doc. Error #187

* New tested wrapper

* Remove automatic addition from my IDE

* Removed automatic IDE addition

* Update bio/bustools/count/environment.yaml

Co-authored-by: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/bustools/count/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bustools =0.41 

bio/bustools/count/meta.yaml

@@ -0,0 +1,20 @@
+name: bustools count
+description: BUS files can be converted into a barcode-feature matrix
+url: https://github.com/BUStools/bustools#count
+author:
+  - Thibault Dayris
+input:
+  - bus: Single bus-file, or List of bus-files
+  - genemap: Transcript to gene mapping
+  - txnames: List of transcripts
+  - ecmap: Equivalence classes for transcripts
+output:
+  - barcodes, equivalence classes, and count matrix
+params:
+  - extra: Optional parameters, besides `--output`, `--ecmap`, and `--genemap`
+notes: |
+  When multiple bus files are provided, only one count matrix is returned.
+
+  When an output endswith: ".hist.txt", then `--hist` parameter is automatically used.
+
+  When an output endswith: ".genes.txt", then `--genemap` parameter is automatically used.

bio/bustools/count/test/Snakefile

@@ -0,0 +1,23 @@
+rule test_bustools_count:
+    input:
+        bus="file.bus",
+        ecmap="matrix.ec",
+        txnames="transcripts.txt",
+        genemap="t2g.txt",
+    output:
+        multiext(
+            "buscount",
+            ".barcodes.txt",
+            ".CUPerCell.txt",
+            ".cu.txt",
+            ".genes.txt",
+            ".hist.txt",
+            ".mtx",
+        ),
+    threads: 1
+    params:
+        extra="",
+    log:
+        "bustools.log",
+    wrapper:
+        "master/bio/bustools/count"

bio/bustools/count/test/matrix.ec

@@ -0,0 +1,20 @@
+0	0
+1	1
+2	2
+3	3
+4	4
+5	5
+6	6
+7	7
+8	8
+9	9
+10	10
+11	11
+12	12
+13	13
+14	6,12
+15	0,1,2
+16	0,1
+17	6,11
+18	3,12
+19	1,2

bio/bustools/count/test/t2g.txt

@@ -0,0 +1,27 @@
+ENST00000282507.7	ENSG00000168671.9
+ENST00000513300.5	ENSG00000168671.9
+ENST00000504685.5	ENSG00000168671.9
+ENST00000504954.1	ENSG00000168671.9
+ENST00000515131.1	ENSG00000168671.9
+ENST00000512916.2	ENSG00000249641.2
+ENST00000243056.4	ENSG00000123364.4
+ENST00000243103.3	ENSG00000123407.3
+ENST00000546378.1	ENSG00000123388.4
+ENST00000243082.4	ENSG00000123388.4
+ENST00000515593.1	ENSG00000180818.4
+ENST00000303460.4	ENSG00000180818.4
+ENST00000511575.1	ENSG00000180818.4
+ENST00000514415.1	ENSG00000180818.4
+ENST00000513413.2	ENSG00000180818.4
+ENST00000504315.1	ENSG00000197757.7
+ENST00000509328.1	ENSG00000197757.7
+ENST00000394331.3	ENSG00000197757.7
+ENST00000243108.4	ENSG00000197757.7
+ENST00000504557.1	ENSG00000180806.4
+ENST00000508190.1	ENSG00000180806.4
+ENST00000303450.4	ENSG00000180806.4
+ENST00000040584.5	ENSG00000037965.5
+ENST00000303406.4	ENSG00000198353.7
+ENST00000507650.1	ENSG00000198353.7
+ENST00000430889.2	ENSG00000198353.7
+ENST00000312492.2	ENSG00000172789.3

bio/bustools/count/test/transcripts.txt

@@ -0,0 +1,14 @@
+ENST00000513300.5
+ENST00000282507.7
+ENST00000504685.5
+ENST00000243108.4
+ENST00000303450.4
+ENST00000243082.4
+ENST00000303406.4
+ENST00000303460.4
+ENST00000243056.4
+ENST00000312492.2
+ENST00000040584.5
+ENST00000430889.2
+ENST00000394331.3
+ENST00000243103.3

bio/bustools/count/wrapper.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+"""Snakemake wrapper for bustools count"""
+
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2022, Thibault Dayris"
+__email__ = "thibault.dayris@gustaveroussy.fr"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+from os.path import commonprefix
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+# Get IO files and prefixes
+bus_files = snakemake.input["bus"]
+if isinstance(bus_files, list):
+    bus_files = " ".join(bus_files)
+
+out_prefix = commonprefix(snakemake.output)[:-1]
+
+# Fill extra parameters if needed
+extra = snakemake.params.get("extra", "")
+if any(outfile.endswith(".hist.txt") for outfile in snakemake.output):
+    if "--hist" not in extra:
+        extra += " --hist"
+
+if any(outfile.endswith(".genes.txt") for outfile in snakemake.output):
+    if "--genecounts" not in extra:
+        extra += " --genecounts"
+
+shell(
+    "bustools count {extra} "
+    "--output {out_prefix} "
+    "--genemap {snakemake.input.genemap} "
+    "--ecmap {snakemake.input.ecmap} "
+    "--txnames {snakemake.input.txnames} "
+    "{bus_files} "
+    "{log}"
+)

test.py

@@ -258,6 +258,12 @@ def test_open_cravat_run():
         ["snakemake", "--cores", "1", "--use-conda"],
     )
 
+@skip_if_not_modified
+def test_bustools_count():
+    run(
+        "bio/bustools/count",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "buscount.mtx"]
+    )
 
 @skip_if_not_modified
 def test_open_cravat_module():