Include pharokka -> phold with plot

.tests/e2e/test_full_run.py

@@ -13,6 +13,9 @@ def setup(tmp_path):
     blast_db_fp = tmp_path / "blast_db"
     blast_db_fp.mkdir(parents=True, exist_ok=True)
     (blast_db_fp / "db.faa").touch()
+    pharokka_dp_fp = tmp_path / "pharokka_db"
+    pharokka_dp_fp.mkdir(parents=True, exist_ok=True)
+    (pharokka_dp_fp / ".installed").touch()
     phold_db_fp = tmp_path / "phold_db"
     phold_db_fp.mkdir(parents=True, exist_ok=True)
     (phold_db_fp / "phold_annots.tsv").touch()
@@ -56,6 +59,17 @@ def setup(tmp_path):
         ]
     )
 
+    config_str = f"sbx_induceome: {{pharokka_dp: {pharokka_dp_fp}}}"
+    sp.check_output(
+        [
+            "sunbeam",
+            "config",
+            "--modify",
+            f"{config_str}",
+            f"{config_fp}",
+        ]
+    )
+
     config_str = f"sbx_induceome: {{phold_db: {phold_db_fp}}}"
     sp.check_output(
         [
@@ -87,6 +101,11 @@ def run_sunbeam(setup):
             "--directory",
             tmp_path,
             "-n",
+            "--include",
+            "sbx_induceome",
+            "--include",
+            "sbx_assembly",
+            "--show-failed-logs",
         ],
         capture_output=True,
         text=True,

README.md

@@ -3,7 +3,7 @@
 # sbx_induceome
 
 <!-- Badges start -->
-[![Tests](https://github.com/Ulthran/sbx_induceome/actions/workflows/tests.yml/badge.svg)](https://github.com/Ulthran/sbx_induceome/actions/workflows/tests.yml)
+[![Tests](https://github.com/sunbeam-labs/sbx_induceome/actions/workflows/tests.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_induceome/actions/workflows/tests.yml)
 ![Condabot](https://img.shields.io/badge/condabot-active-purple)
 [![DockerHub](https://img.shields.io/docker/pulls/sunbeamlabs/sbx_induceome)](https://hub.docker.com/repository/docker/sunbeamlabs/sbx_induceome/)
 <!-- Badges end -->
@@ -20,6 +20,7 @@ NOTE: sbx_induceome makes a couple assumptions about your reference genomes and
   - reference_fp: Directory with reference genomes
   - mapping_fp: Path to the file mapping samples to strains (.csv)
   - blast_db: Path to the viral blast db (full path including .faa file name)
+  - pharokka_db: Path to the pharokka db (full path to the directory that will hold db files)
   - phold_db: Path to the phold db (full path to the directory that will hold the tsv and other db files)
   - min_width: The sliding window size for peak finding
   - smoothing_factor: The number of below-threshold sliding windows to tolerate as being part of one peak

config.yml

@@ -3,6 +3,7 @@ sbx_induceome:
   reference_fp: /path/to/refs/
   mapping_fp: /path/to/mapping.csv
   blast_db: /path/to/blast/db.faa
+  pharokka_db: /path/to/pharokka/db/
   phold_db: /path/to/phold/db/
   min_width: 100
   smoothing_factor: 10

sbx_induceome.smk

@@ -64,7 +64,7 @@ rule all_induceome:
         expand(INDUCEOME_FP / "peaks" / "{sample}.csv", sample=SBX_INDUCEOME_SAMPLES),
         expand(INDUCEOME_FP / "blastx" / "{sample}.btf", sample=SBX_INDUCEOME_SAMPLES),
         expand(
-            INDUCEOME_FP / "phold" / "{sample}_compare" / "phold.gbk",
+            INDUCEOME_FP / "phold" / "{sample}_plot" / "phold.png",
             sample=SBX_INDUCEOME_SAMPLES,
         ),
 
@@ -215,20 +215,56 @@ rule induceome_blastx:
 
 
 ###
-# PHOLD
+# PHAROKKA/PHOLD/PHYNTENY
 ###
 
 
-rule induceome_install_phold_database:
+rule induceome_install_ph_databases:
     output:
+        pharokka=Path(Cfg["sbx_induceome"]["pharokka_db"])
+        / "pharokka_db"
+        / ".installed",
         annotations=Path(Cfg["sbx_induceome"]["phold_db"]) / "phold_annots.tsv",
+    benchmark:
+        BENCHMARK_FP / "induceome_install_ph_databases.tsv"
+    log:
+        LOG_FP / "induceome_install_ph_databases.log",
+    conda:
+        "envs/sbx_induceome_env.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_induceome:{SBX_INDUCEOME_VERSION}"
+    shell:
+        """
+        echo "Installing pharokka database" > {log}
+        install_databases.py -o $(dirname {output.pharokka}) >> {log} 2>&1
+        touch {output.pharokka}
+
+        echo "Installing phold annotations" >> {log}
+        phold install --database $(dirname {output.annotations}) >> {log} 2>&1
+        """
+
+
+rule induceome_pharokka:
+    input:
+        contigs=ASSEMBLY_FP / "megahit" / "{sample}_asm" / "final.contigs.fa",
+        pharokka_db=Path(Cfg["sbx_induceome"]["pharokka_db"]) / "pharokka_db",
+    output:
+        pharokka_gbk=INDUCEOME_FP / "pharokka" / "{sample}_pharokka.gbk",
+    benchmark:
+        BENCHMARK_FP / "induceome_pharokka_{sample}.tsv"
+    log:
+        LOG_FP / "induceome_pharokka_{sample}.log",
     conda:
         "envs/sbx_induceome_env.yml"
     container:
         f"docker://sunbeamlabs/sbx_induceome:{SBX_INDUCEOME_VERSION}"
     shell:
         """
-        phold install --database $(dirname {output.annotations})
+        if [ ! -s {input.contigs} ]; then
+            touch {output.pharokka_gbk}
+        else
+            pharokka run -i {input.contigs} -o $(dirname {output.pharokka_gbk}) --database {input.pharokka_db} --force
+        fi
         """
 
 
@@ -280,3 +316,22 @@ rule induceome_phold_compare:
             phold compare -i {input.contigs} --predictions_dir $(dirname {input._3di}) -o $(dirname {output.gbk}) --database $(dirname {input.annotations}) -t 8 --force
         fi
         """
+
+
+rule induceome_phold_plot:
+    input:
+        gbk=INDUCEOME_FP / "phold" / "{sample}_compare" / "phold.gbk",
+    output:
+        png=INDUCEOME_FP / "phold" / "{sample}_plot" / "phold.png",
+    benchmark:
+        BENCHMARK_FP / "induceome_phold_plot_{sample}.tsv"
+    log:
+        LOG_FP / "induceome_phold_plot_{sample}.log",
+    conda:
+        "envs/sbx_induceome_env.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_induceome:{SBX_INDUCEOME_VERSION}"
+    shell:
+        """
+        phold plot -i {input.gbk} -o $(dirname {output.png}) --force
+        """