Added config module and used it in the module scripts

bin/config.py

+import os
+import yaml
+
+def get_install_location():
+    """Finds the location directory of the tool"""
+    script_path = os.path.realpath(__file__)
+    script_dir = os.path.dirname(script_path)
+    install_dir = os.path.dirname(script_dir)
+    return install_dir
+
+def get_script_location():
+    return os.path.join(get_install_location(),'bin')
+
+def get_template_location():
+    return os.path.join(get_install_location(),'templates')
+
+def get_modules_location():
+    return os.path.join(get_install_location(),'modules')
+
+def get_profiles_location():
+    return os.path.join(get_install_location(),'profiles')
+
+def get_config_file():
+    return os.path.join(get_install_location(), 'config.yaml')
+
+def load_config_file():
+    config = {}
+    with (open(get_config_file())) as f:
+        config = yaml.load(f)
+    return config
+
+def get_module_manifests():
+    mypath = get_modules_location()
+    return [os.path.join(mypath, f) for f in os.listdir(mypath) if os.path.isfile(os.path.join(mypath, f))]
+        
+def load_modules():
+    modules = []
+    for manifest in get_module_manifests():
+        with (open(manifest)) as f:
+            modules.append(yaml.load(f))
+    return modules
+
+def load_config():
+    config = load_config_file()
+    config['modules'] = load_modules()
+    return config
+
+if __name__ == "__main__":
+    """prints the configuration"""
+    import config
+    from pprint import pformat
+
+    print('Install location: ' + config.get_install_location())
+    print('Script lcoation: ' + config.get_script_location())
+    print('Config location: ' + config.get_config_file())
+    print('Available module manifests:\n\t' + '\n\t'.join(config.get_module_manifests()) + '\n')
+    print('Config content:\n' + pformat(config.load_config_file()) + '\n')
+    print('Manifest content:\n' + pformat(config.load_modules()) + '\n')
+
+    print('Aggregated config:\n' + pformat(config.load_config()) + '\n')
+

bin/module_blast_swissprot.py

 #!/usr/bin/env python3
 import argparse
-import yaml
-import os
+import config
 from os import system
 
-def get_config_file():
-    """Finds the config file, that is located in the directory above script"""
-    script_path = os.path.realpath(__file__)
-    script_dir = os.path.dirname(script_path)
-    config_dir = os.path.dirname(script_dir)
-    config_file = os.path.join(config_dir, 'config.yaml')
-    return config_file
-
-def get_blastp_tool():
-    """Extracts the configuration entry for blastp. If it is not present, it defaults to blastp"""
-    tool = None
-    with open(get_config_file()) as f: 
-        config = yaml.load(f)
-        tool = config['tools'].get('blastp', 'blastp')
-    return tool
-
+blastp_tool = config.load_config()['tools'].get('blastp', 'blastp')
 
 parser = argparse.ArgumentParser(description='Identify homologues in the swissprot database')
+parser.add_argument('--info', '-i', action='store_true')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
 parser.add_argument('--evalue', '-e', default='0.0001', help='Evalue cutoff')
 parser.add_argument('--alignment', '-a', action='store_true', help='Include alignments in btop format')
 
 args = parser.parse_args()
+if args.info:
+    print("blast against swissprot\n")
+    exit(0)
 
 format = '7 qseqid sseqid pident qstart qend sstart send evalue bitscore'
 if args.alignment:
     format += ' btop'
 
-system(get_blastp_tool() + " -db /vol/biodb/uniprot/uniprot_sprot.fasta -num_threads 7 -outfmt '" + format + "' -out - -query " + args.fasta)
+system(blastp_tool + " -db /vol/biodb/uniprot/uniprot_sprot.fasta -num_threads 7 -outfmt '" + format + "' -out - -query " + args.fasta)

bin/module_signalp.py

 #!/usr/bin/env python3
 import argparse
-import yaml
-import os
+import config
 from os import system
 
-def get_config_file():
-    """Finds the config file, that is located in the directory above script"""
-    script_path = os.path.realpath(__file__)
-    script_dir = os.path.dirname(script_path)
-    config_dir = os.path.dirname(script_dir)
-    config_file = os.path.join(config_dir, 'config.yaml')
-    return config_file
-
-def get_signalp_tool():
-    """Extracts the configuration entry for signalp. If it is not present, it defaults to signalp"""
-    tool = None
-    with open(get_config_file()) as f: 
-        config = yaml.load(f)
-        tool = config['tools'].get('signalp', 'signalp')
-    return tool
-
+signalp_tool = config.load_config()['tools'].get('signalp', 'signalp')
 
 parser = argparse.ArgumentParser(description='Find signal peptides in amino acid sequences')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
 parser.add_argument('--organism', '-o', choices=['euk', 'gram+', 'gram-'], default='euk', help='The organism type')
 args = parser.parse_args()
 
-system(get_signalp_tool() + " -t " + args.organism + " " + args.fasta)
+system(signalp_tool + " -t " + args.organism + " " + args.fasta)