Include MOB_suite for Plasmid prediction | modify MGE prediction

01b6b60d · Laura Denies · 223aa6a5 · 01b6b60d · 01b6b60d · 01b6b60d
Commit 01b6b60d authored Jun 18, 2020 by Laura Denies
--- a/envs/DeepVirFinder.yaml
+++ b/envs/DeepVirFinder.yaml
 channels:
-  - conda-forge
  - bioconda
+  - conda-forge
  - defaults
 dependencies:
  - _libgcc_mutex=0.1=main
@@ -33,7 +33,7 @@ dependencies:
  - libgcc-ng=9.1.0=hdf63c60_0
  - libgfortran-ng=7.3.0=hdf63c60_0
  - libgpuarray=0.7.6=h14c3975_1003
-    - liblapack=3.8.0=12_openblas
+  - liblapack=3.8.0=12_openblas
  - libopenblas=0.3.7=h6e990d7_1
  - libprotobuf=3.9.2=h8b12597_0
  - libstdcxx-ng=9.1.0=hdf63c60_0
@@ -69,4 +69,5 @@ dependencies:
  - wrapt=1.11.2=py36h516909a_0
  - xz=5.2.4=h14c3975_1001
  - yaml=0.1.7=h14c3975_1001
-  - zlib=1.2.11=h516909a_1006
\ No newline at end of file
+  - zlib=1.2.11=h516909a_1006
+
--- a/envs/MOB_suite.yaml
+++ b/envs/MOB_suite.yaml
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_llvm
+  - biopython=1.76=py38h516909a_0
+  - blast=2.5.0=hc0b0e79_3
+  - blosc=1.19.0=he1b5a44_0
+  - boost=1.73.0=py38hd103949_0
+  - boost-cpp=1.73.0=h6c875cf_0
+  - bzip2=1.0.8=h516909a_2
+  - ca-certificates=2020.4.5.2=hecda079_0
+  - capnproto=0.6.1=hfc679d8_1
+  - certifi=2020.4.5.2=py38h32f6830_0
+  - dbus=1.13.6=he372182_0
+  - ete3=3.1.1=pyh9f0ad1d_2
+  - expat=2.2.9=he1b5a44_2
+  - fontconfig=2.13.1=h86ecdb6_1001
+  - freetype=2.10.2=he06d7ca_0
+  - gettext=0.19.8.1=hc5be6a0_1002
+  - glib=2.64.3=h6f030ca_0
+  - gsl=2.5=h294904e_1
+  - gst-plugins-base=1.14.5=h0935bb2_2
+  - gstreamer=1.14.5=h36ae1b5_2
+  - hdf5=1.10.6=nompi_h3c11f04_100
+  - icu=64.2=he1b5a44_1
+  - jpeg=9d=h516909a_0
+  - krb5=1.17.1=h2fd8d38_0
+  - ld_impl_linux-64=2.34=h53a641e_5
+  - libblas=3.8.0=16_openblas
+  - libcblas=3.8.0=16_openblas
+  - libclang=9.0.1=default_hde54327_0
+  - libcurl=7.69.1=hf7181ac_0
+  - libedit=3.1.20191231=h46ee950_0
+  - libffi=3.2.1=he1b5a44_1007
+  - libgcc-ng=9.2.0=h24d8f2e_2
+  - libgfortran-ng=7.5.0=hdf63c60_6
+  - libiconv=1.15=h516909a_1006
+  - liblapack=3.8.0=16_openblas
+  - libllvm9=9.0.1=he513fc3_1
+  - libopenblas=0.3.9=h5ec1e0e_0
+  - libpng=1.6.37=hed695b0_1
+  - libssh2=1.9.0=hab1572f_2
+  - libstdcxx-ng=9.2.0=hdf63c60_2
+  - libuuid=2.32.1=h14c3975_1000
+  - libxcb=1.13=h14c3975_1002
+  - libxkbcommon=0.10.0=he1b5a44_0
+  - libxml2=2.9.10=hee79883_0
+  - libxslt=1.1.33=h31b3aaa_0
+  - llvm-openmp=10.0.0=hc9558a2_0
+  - lxml=4.5.1=py38hbb43d70_0
+  - lz4-c=1.9.2=he1b5a44_1
+  - lzo=2.10=h14c3975_1000
+  - mash=2.2.2=h3d38be6_1
+  - mob_suite=3.0.0=py_1
+  - mock=4.0.2=py38h32f6830_0
+  - ncurses=6.1=hf484d3e_1002
+  - nspr=4.25=he1b5a44_0
+  - nss=3.47=he751ad9_0
+  - numexpr=2.7.1=py38hcb8c335_1
+  - numpy=1.18.5=py38h8854b6b_0
+  - openssl=1.1.1g=h516909a_0
+  - pandas=1.0.4=py38hcb8c335_0
+  - pcre=8.44=he1b5a44_0
+  - pip=20.1.1=py_1
+  - pthread-stubs=0.4=h14c3975_1001
+  - pycurl=7.43.0.5=py38h16ce93b_0
+  - pyqt=5.12.3=py38ha8c2ead_3
+  - pytables=3.6.1=py38h1b207d3_2
+  - python=3.8.3=cpython_he5300dc_0
+  - python-dateutil=2.8.1=py_0
+  - python_abi=3.8=1_cp38
+  - pytz=2020.1=pyh9f0ad1d_0
+  - qt=5.12.5=hd8c4c69_1
+  - readline=8.0=hf8c457e_0
+  - scipy=1.4.1=py38h18bccfc_3
+  - setuptools=47.1.1=py38h32f6830_0
+  - six=1.15.0=pyh9f0ad1d_0
+  - sqlite=3.30.1=hcee41ef_0
+  - tk=8.6.10=hed695b0_0
+  - wheel=0.34.2=py_1
+  - xorg-kbproto=1.0.7=h14c3975_1002
+  - xorg-libice=1.0.10=h516909a_0
+  - xorg-libsm=1.2.3=h84519dc_1000
+  - xorg-libx11=1.6.9=h516909a_0
+  - xorg-libxau=1.0.9=h14c3975_0
+  - xorg-libxdmcp=1.1.3=h516909a_0
+  - xorg-libxext=1.3.4=h516909a_0
+  - xorg-libxrender=0.9.10=h516909a_1002
+  - xorg-renderproto=0.11.1=h14c3975_1002
+  - xorg-xextproto=7.3.0=h14c3975_1002
+  - xorg-xproto=7.0.31=h14c3975_1007
+  - xz=5.2.5=h516909a_0
+  - zlib=1.2.11=h516909a_1006
+  - zstd=1.4.4=h6597ccf_3
+  - pip:
+    - pyqt5-sip==4.19.18
+    - pyqtchart==5.12
+    - pyqtwebengine==5.12.1
+
--- a/rules/AMR/Combine_MGE_AMR.smk
+++ b/rules/AMR/Combine_MGE_AMR.smk
@@ -11,7 +11,7 @@ rule combine_AMR_plasmid:
    input:
        AMR="{datadir}/{project}/AMR/deepARG_results/{sample}.out.mapping.ARG",
        AMR_translation="{datadir}/{project}/renamed/{sample}_translation.tsv",
-        Plasmid="{datadir}/{project}/MGE/plasmid/{sample}_plasflow_prediction_final.tsv",
+        Plasmid="{datadir}/{project}/MGE/PlasFlow/plasmid/{sample}_plasflow_prediction_final.tsv",
        Contig_translation="{datadir}/{project}/renamed/{sample}_Contig_translation.tsv",
        Contig_gene_list="{datadir}/{project}/Prodigal/{sample}.contig",
        VirFinder="{datadir}/{project}/MGE/phage/{sample}_VirFinder_aggregated.csv",

--- a/rules/AMR/Phage.smk
+++ b/rules/AMR/Phage.smk
@@ -7,26 +7,7 @@ import os
 #     Phage Prediction   #
 ##########################

-# VIRSORTER Preprocessing
-
-checkpoint splitphage:
-    input:
-        "{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
-    output:
-        split=directory("{datadir}/{project}/contig_splitted/{sample}/")
-#    log:
-#        "{datadir}/{project}/contig_splitted/{sample}.log"
-    params:
-        outdir="{datadir}",
-        runtime=config["pathofact"]["runtime"]["medium"],
-        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"],
-        split=config["pathofact"]["size_fasta"]
-    conda:
-        "../../envs/Biopython.yaml"
-    shell:
-        """
-         python {config[pathofact][scripts]}/split.py {input} {params.split} {wildcards.datadir}/{wildcards.project}/contig_splitted/{wildcards.sample}
-        """
+# VIRSORTER 

 rule run_VirSorter:
    input:
@@ -64,9 +45,9 @@ rule run_VirFinder:
    input:
        "{datadir}/{project}/contig_splitted/{sample}/{file_i}.fasta"
    output:
-        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fna_gt1bp_dvfpred.txt"
+        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fasta_gt1bp_dvfpred.txt"
    log:
-        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fna_gt1bp_dvfpred.log"
+        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fasta_gt1bp_dvfpred.log"
    params:
        outdir="{datadir}",
        runtime=config["pathofact"]["runtime"]["long"],
@@ -79,9 +60,9 @@ rule run_VirFinder:
        "python {config[pathofact][deepvirfinder]} -i {input} -o {wildcards.datadir}/{wildcards.project}/MGE/phage/{wildcards.sample}/virfinder -c {threads} &> {log}"

 def aggregate_VirFinder(wildcards):
-    checkpoint_output= checkpoints.splitphage.get(**wildcards).output.split
+    checkpoint_output= checkpoints.splitcontig.get(**wildcards).output.split
    return expand(
-        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fna_gt1bp_dvfpred.txt",
+        "{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fasta_gt1bp_dvfpred.txt",
        datadir=wildcards.datadir,
        project=wildcards.project,
        sample=wildcards.sample,

--- a/rules/AMR/Plasmid.smk
+++ b/rules/AMR/Plasmid.smk
@@ -30,18 +30,16 @@ checkpoint splitplasmid:
        "{datadir}/{project}/{sample}_filtered.fna"
    output:
        split=directory("{datadir}/{project}/MGE/plasmid_splitted/{sample}/")
-    log:
-        "{datadir}/{project}/MGE/plasmid_splitted/{sample}.log"
    params:
        outdir="{datadir}",
-        runtime=config["pathofact"]["runtime"]["medium"],
+        runtime=config["pathofact"]["runtime"]["short"],
        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"],
        split=config["pathofact"]["size_fasta"]
    conda:
        "../../envs/Biopython.yaml"
    shell:
        """
-         python {config[pathofact][scripts]}/split.py {input} {params.split} {wildcards.datadir}/{wildcards.project}/plasmid_splitted/{wildcards.sample}
+         python {config[pathofact][scripts]}/split.py {input} {params.split} {wildcards.datadir}/{wildcards.project}/MGE/plasmid_splitted/{wildcards.sample}
        """

 # PlasFlow Plasmid prediction
@@ -49,9 +47,9 @@ rule run_PLASMID:
    input:
        "{datadir}/{project}/MGE/plasmid_splitted/{sample}/{file_i}.fasta"
    output:
-        temp("{datadir}/{project}/MGE/plasmid/{sample}/{file_i}_plasflow_prediction.tsv")
+        temp("{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_plasflow_prediction.tsv")
    log:
-        "{datadir}/{project}/MGE/plasmid/{sample}/{file_i}_plasflow_prediction.log"
+        "{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_plasflow_prediction.log"
    conda:
        "../../envs/PlasFlow.yaml"
    params:
@@ -67,7 +65,7 @@ rule run_PLASMID:
 def aggregate_plasmid_input(wildcards):
    checkpoint_output= checkpoints.splitplasmid.get(**wildcards).output.split
    return expand(
-        "{datadir}/{project}/MGE/plasmid/{sample}/{file_i}_plasflow_prediction.tsv",
+        "{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_plasflow_prediction.tsv",
        datadir=wildcards.datadir,
        project=wildcards.project,
        sample=wildcards.sample,
@@ -78,7 +76,7 @@ rule Plasmid_aggregate:
    input:
        aggregate_plasmid_input
    output:
-        "{datadir}/{project}/MGE/plasmid/{sample}_plasflow_aggregated.tsv"
+        "{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_aggregated.tsv"
    params:
        outdir="{datadir}",
        runtime=config["pathofact"]["runtime"]["short"],
@@ -88,9 +86,9 @@ rule Plasmid_aggregate:

 rule select:
    input:
-        "{datadir}/{project}/MGE/plasmid/{sample}_plasflow_aggregated.tsv"
+        "{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_aggregated.tsv"
    output:
-        "{datadir}/{project}/MGE/plasmid/{sample}_plasflow_prediction_final.tsv"
+        "{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_prediction_final.tsv"
    params:
        outdir="{datadir}",
        runtime=config["pathofact"]["runtime"]["short"],
@@ -99,3 +97,40 @@ rule select:
        """
        cut -f 3,6 {input} > {output}
        """
+
+rule run_MOBsuite:
+    input: "{datadir}/{project}/contig_splitted/{sample}/{file_i}.fasta"
+    output:         
+        temp("{datadir}/{project}/MGE/plasmid/MOB_suite/{sample}/{file_i}_MOB_suite_prediction.txt")
+    log:
+        "{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_MOB_suite_prediction.log"
+    params: 
+        outdir="{datadir}",
+	runtime=config["pathofact"]["runtime"]["long"]
+    threads:
+        config["pathofact"]["mem"]["big_mem_cores"]
+    conda:
+        "../../envs/MOB_suite.yaml"
+    shell: "mob_typer --multi --infile {input} --out_file {wildcards.datadir}/{wildcards.project}/MGE/plasmid/MOB_suite/{wildcards.sample}/{wildcards.file_i}_MOB_suite_prediction.txt -n {threads}"
+
+def aggregate_MOBsuite(wildcards):
+    checkpoint_output= checkpoints.splitcontig.get(**wildcards).output.split
+    return expand(
+        "{datadir}/{project}/MGE/plasmid/MOB_suite/{sample}/{file_i}_MOB_suite_prediction.txt",
+        datadir=wildcards.datadir,
+        project=wildcards.project,
+        sample=wildcards.sample,
+        file_i=glob_wildcards(os.path.join(checkpoint_output, "{i}.fasta")).i
+    )
+
+rule aggregate_MOBsuite:
+    input: aggregate_MOBsuite
+    output:
+        "{datadir}/{project}/MGE/plasmid/MOB_suite/{sample}_MOB_suite_aggregated.tsv"
+    params:
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["short"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
+    shell:
+        "cat {input} > {output}"
+
--- a/rules/Universal/Preprocessing_contig.smk
+++ b/rules/Universal/Preprocessing_contig.smk
@@ -41,3 +41,22 @@ rule generate_ContigTranslation:
        """
        paste {input.renamed} {input.original} | awk 'sub(/^>/,"")' OFS='\\t' > {output}
        """
+
+checkpoint splitcontig:
+    input:
+        "{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
+    output:
+        split=directory("{datadir}/{project}/contig_splitted/{sample}/")
+    params:
+        outdir="{datadir}",
+        runtime=config["pathofact"]["runtime"]["short"],
+        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"],
+        split=config["pathofact"]["size_fasta"]
+    conda:
+        "../../envs/Biopython.yaml"
+    shell:
+        """
+         python {config[pathofact][scripts]}/split.py {input} {params.split} {wildcards.datadir}/{wildcards.project}/contig_splitted/{wildcards.sample}
+        """
+
+
--- a/run_PathoFact.sh
+++ b/run_PathoFact.sh
+#!/bin/bash -l
+
+conda activate snakemake
+
+snakemake -s Snakefile --use-conda --rerun-incomplete --cores 28 -p
--- a/workflows/AMR_workflow.smk
+++ b/workflows/AMR_workflow.smk
@@ -19,7 +19,8 @@ rule AMR_Analysis:
            [
                "{datadir}/{project}/MGE/phage/{sample}_VIRSorter_aggregated.csv",
                "{datadir}/{project}/MGE/phage/{sample}_VirFinder_aggregated.csv",
-                "{datadir}/{project}/MGE/plasmid/{sample}_plasflow_prediction_final.tsv", 
+                "{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_prediction_final.tsv", 
+                "{datadir}/{project}/MGE/plasmid/MOB_suite/{sample}_MOB_suite_aggregated.tsv"
                "{datadir}/{project}/AMR_MGE_prediction_{sample}_report.tsv",        
                "{datadir}/{project}/AMR/{sample}_AMR_MGE_prediction_detailed.tsv"
           ],