current RIMA Kraken version

Author: Lin Yang

metasheet.csv

@@ -0,0 +1,223 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import subprocess
+import pandas as pd
+import yaml
+
+from string import Template
+#from snakemake_files.scripts.utils import getTargetInfo
+
+def getRuns(config):
+    ret = {}
+    #LEN: Weird, but using pandas to handle the comments in the file
+    #KEY: need skipinitialspace to make it fault tolerant to spaces!
+    metadata = pd.read_csv(config['metasheet'], index_col=0, sep=',', comment='#', skipinitialspace=True)
+    f = metadata.to_csv().split() #make it resemble an actual file with lines
+    #SKIP the hdr
+    for l in f[1:]:
+        tmp = l.strip().split(",")
+        #print(tmp)
+        ret[tmp[0]] = tmp[1:]
+        #print(ret)
+        config['runs'] = ret
+    return config
+
+# def addCondaPaths_Config(config):
+#     """ADDS the python2 paths to config"""
+#     conda_root = subprocess.check_output('conda info --root',shell=True).decode('utf-8').strip()
+#     config['conda_root'] = conda_root
+#     config['wes_root'] = "%s/envs/wes" % conda_root
+
+def addCondaPaths_Config(config):
+    """ADDS the python2 paths to config"""
+    conda_root = subprocess.check_output('conda info --root',shell=True).decode('utf-8').strip()
+    conda_path = os.path.join(conda_root, 'pkgs')
+    current_path = os.getcwd()
+    config['conda_root'] = conda_root
+    config['rnaseq_root'] = "%s/envs/rna" % conda_root
+    config['stat_root'] = "%s/envs/stat_perl_r" % conda_root
+    config['centrifuge_root']= "/%s/envs/centrifuge_env" % conda_root
+    config['rseqc_root']= "%s/envs/rseqc_env" % conda_root
+    config['gatk4_root']= "/%s/envs/gatk4_env" % conda_root
+    config['msisensor_root']= "/%s/envs/msisensor_env" % conda_root
+    config['vep_root']= "/%s/envs/vep_env" % conda_root
+    config['varscan_root']= "/%s/envs/varscan_env" % conda_root
+    config['immnue_decov']= "%s/envs/imm_env" % conda_root
+    config['trust4_env']= "%s/envs/trust4_env" % conda_root
+    config['mMCP_env']= "%s/envs/mMCP_env" % conda_root
+    config['pvacseq'] = "%s/envs/pvacseq" % conda_root
+
+    
+def addExecPaths(config):
+    conda_root = subprocess.check_output('conda info --root',shell=True).decode('utf-8').strip()
+    conda_path = os.path.join(conda_root, 'pkgs')
+    current_path = os.getcwd()
+    TRUST4_path = "/liulab/RIMA_kraken"
+    arcasHLA_path = "/liulab/linyang"
+    #NEED the following when invoking python2 (to set proper PYTHONPATH)
+    if not "pvacseq_path" in config or not config["pvacseq_path"]:
+        config["pvacseq_path"] = os.path.join(conda_root, 'envs', 'pvacseq', 'bin')
+    if not "trust4_path" in config or not config["trust4_path"]:
+        config["trust4_path"] = os.path.join(TRUST4_path,'TRUST4')
+    if not "arcasHLA_path" in config or not config["arcasHLA_path"]:
+        config["arcasHLA_path"] = os.path.join(arcasHLA_path,'arcasHLA')
+    if not "msisensor2_path" in config or not config["msisensor2_path"]:
+        config["msisensor2_path"] = os.path.join(TRUST4_path,'msisensor2')
+    return config
+
+def loadRef(config):
+    f = open(config['ref'])
+    ref_info = yaml.safe_load(f)
+    f.close()
+    #print(ref_info[config['assembly']])
+    for (k,v) in ref_info[config['assembly']].items():
+    #NO CLOBBERING what is user-defined!
+        if k not in config:
+            config[k] = v
+
+def load_config(config_file):
+    #load the main config file including parameters which are not change a lot
+    with open(config_file, 'r') as stream:
+        try:
+            return yaml.safe_load(stream)
+        except yaml.YAMLError as exc:
+            print(exc)
+
+def load_execution(execution_file):
+    #load the main config file including parameters which are not change a lot
+    with open(execution_file, 'r') as stream:
+        try:
+            return yaml.safe_load(stream)
+        except yaml.YAMLError as exc:
+            print(exc)
+
+#---------  CONFIG set up  ---------------
+config = load_config('config.yaml')
+execution = load_execution('execution.yaml')
+addCondaPaths_Config(config)
+#config = getRuns(config)
+loadRef(config)
+addExecPaths(config)
+
+
+
+
+#------------------------------------------------------------------------------
+# TARGETS
+#------------------------------------------------------------------------------
+def all_targets(wildcards):
+    ls = []
+    #------------------------------------------------------------------------
+    ##Level1
+    #------------------------------------------------------------------------
+    if execution["star"]:
+        ls.extend(align_targets(wildcards))
+        ls.extend(star_report_tagets(wildcards))
+    if execution["salmon"]:
+        ls.extend(salmon_targets(wildcards))
+    if execution["rseqc"]:
+        ls.extend(rseqc_targets(wildcards))
+    #-----------------------------------------------------------------------
+    ##Level2
+    #----------------------------------------------------------------------
+    if execution["batch_removal"]:
+        ls.extend(combat_targets(wildcards))
+    if execution["deseq2"]:
+        ls.extend(deseq2_targets(wildcards))
+    if execution["gsea"]:
+        ls.extend(gsea_targets(wildcards))
+    if execution["ssgsea"]:
+        ls.extend(ssgsea_targets(wildcards))
+    #--------------------------------------------------------------------    
+    ##Level3
+    #--------------------------------------------------------------------
+ #   if execution["fusion"]:
+ #       ls.extend(fusion_targets(wildcards))
+    if execution["microbiota"]:
+        ls.extend(microbe_targets(wildcards))
+    if execution["trust4"]:
+        ls.extend(trust4_targets(wildcards))
+    if execution["arcasHLA"]:
+        ls.extend(arcasHLA_targets(wildcards))
+    #---------------------------------------------------------------------    
+    ##Level4
+    #---------------------------------------------------------------------
+#    if execution["tide"]:
+#        ls.extend(tide_targets(wildcards))
+    if execution["immunedeconv"]:
+        ls.extend(immunedeconv_targets(wildcards))
+    if execution["mMCP"]:
+        ls.extend(mMCP_targets(wildcards))
+    #-------------------------------------------------------------------
+    ##Level5
+    #-------------------------------------------------------------------
+    if execution["msisensor2"]:
+        ls.extend(msisensor_targets(wildcards))
+    if execution["report"]:
+        ls.extend(report_targets(wildcards))
+    if execution["pvacseq"]:
+        ls.extend(neoantigen_targets(wildcards))
+
+    return ls
+
+rule target:
+    input: 
+        all_targets
+    message: "Compiling all output"
+
+ ##Level1   
+if execution["star"]:
+    include: "./snakemake_files/level1/star_final.snakefile"
+if execution["salmon"]:
+    include: "./snakemake_files/level1/salmon_final.snakefile"
+if execution["rseqc"]:
+    include: "./snakemake_files/level1/rseqc_final.snakefile"
+##Level2
+if execution["batch_removal"]:
+    include: "./snakemake_files/level2/batch_removal.snakefile"
+if execution["deseq2"]:
+    include: "./snakemake_files/level2/deseq2.modified.snakefile"
+if execution["gsea"]:
+    include: "./snakemake_files/level2/gsea.modified.snakefile"
+if execution["ssgsea"]:
+    include: "./snakemake_files/level2/ssgsea_final.snakefile"
+##Level3
+#if execution["fusion"]:
+#    include: "./snakemake_files/level3_individual.snakefile"
+if execution["microbiota"]:
+    include: "./snakemake_files/level3/microbiota_final.snakefile"
+if execution["trust4"]:
+    include: "./snakemake_files/level3/trust4_final.snakefile"
+if execution["arcasHLA"]:
+    include: "./snakemake_files/level3/arcasHLA.snakefile"
+##Level4
+#if execution["tide"]:
+#    include: "./snakemake_files/level4/tide.snakefile"
+if execution["immunedeconv"]:
+    include: "./snakemake_files/level4/immunedeconv.snakefile"
+if execution["mMCP"]:
+    include: "./snakemake_files/level4/mMCP.snakefile"
+##Level5
+if execution["msisensor2"]:
+    include: "./snakemake_files/level5/msisensor.snakefile"
+if execution["report"]:
+    include: "./snakemake_files/report.snakefile"
+if execution["pvacseq"]:
+    include: "./snakemake_files/level5/pvacseq_final.snakefile"
+
+    
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