Change to 4-space indentation, PEP-8.

Remove deprecated WSDL files.
Make example use only web services.

Author: pansapiens

examples/surfg/summarize.py

@@ -2,7 +2,6 @@
 import os
 import glob
 
-
 names = """
 AE004092 Streptococcus pyogenes 
 AE017198 Lactobacillus johnsonii
@@ -11,17 +10,16 @@
 CR954253 Lactobacillus delbrueckii 
 """
 tokens = [l.split() for l in names.splitlines()]
-gbk = { ts[0]: ' '.join(ts[1:]) for ts in tokens if ts}
-
+gbk = {ts[0]: ' '.join(ts[1:]) for ts in tokens if ts}
 
 for genome in gbk:
     pse = genome + '.pse'
     if not os.path.isfile(pse):
-      os.system("python ../../inmembrane.py %s.fasta > %s" % (genome, pse))
+        os.system("python ../../inmembrane.py %s.fasta > %s" % (genome, pse))
 
     print "%s: %s" % (genome, gbk[genome])
     print "--"
-    
+
     category_count = {}
     for line in open(pse):
         if line.startswith("#"):
@@ -37,7 +35,7 @@
     category_count["TOTAL"] = n
     for category in ['CYTOPLASM', 'MEMBRANE', 'PSE', 'SECRETED', 'TOTAL']:
         count = category_count[category]
-        percent = 100.0*count/float(n)
+        percent = 100.0 * count / float(n)
         print "%-9s %4d %3.f%%" % (category, count, percent)
 
     print

inmembrane/__init__.py

@@ -2,6 +2,7 @@
 import helpers
 
 import os, shutil
+
 module_dir = os.path.abspath(os.path.dirname(__file__))
 
 default_params_str = """{
@@ -37,146 +38,149 @@
 }
 """
 
+
 def get_params():
-  from helpers import log_stderr
-  """
-  Gets the params dictionary that hold all the configuration
-  information of the program. This is loaded from 'inmembrane.config'
-  which should be found in the same place as the main binary.
-
-  If 'inmembrane.config' is not a found, a default 'inmembrane.config'
-  is generated from 'default_params_str'. The config file should
-  be edited if the binaries are not available on the path, or have
-  different names.
-  """
-  config = os.path.join(os.getcwd(), 'inmembrane.config')
-  if not os.path.isfile(config):
-    log_stderr("# Couldn't find inmembrane.config file")
-    log_stderr("# So, will generate a default config " + config)
-    abs_hmm_profiles = os.path.join(module_dir, 'hmm_profiles')
-    fh = open(config, 'w')
-    fh.write(default_params_str)
-    fh.close()
-  else:
-    log_stderr("# Loading existing inmembrane.config")
-  params = eval(open(config).read())
-  return params
+    from helpers import log_stderr
+    """
+    Gets the params dictionary that hold all the configuration
+    information of the program. This is loaded from 'inmembrane.config'
+    which should be found in the same place as the main binary.
+  
+    If 'inmembrane.config' is not a found, a default 'inmembrane.config'
+    is generated from 'default_params_str'. The config file should
+    be edited if the binaries are not available on the path, or have
+    different names.
+    """
+    config = os.path.join(os.getcwd(), 'inmembrane.config')
+    if not os.path.isfile(config):
+        log_stderr("# Couldn't find inmembrane.config file")
+        log_stderr("# So, will generate a default config " + config)
+        abs_hmm_profiles = os.path.join(module_dir, 'hmm_profiles')
+        fh = open(config, 'w')
+        fh.write(default_params_str)
+        fh.close()
+    else:
+        log_stderr("# Loading existing inmembrane.config")
+    params = eval(open(config).read())
+    return params
+
 
 def init_output_dir(params):
-  """
-  Creates a directory for all output files and makes it the current 
-  working directory. copies the input sequences into it as 'input.fasta'.
-  """
-  from helpers import dict_get
-  
-  if dict_get(params, 'out_dir'):
-    base_dir = params['out_dir']
-  else:
-    base_dir = '.'.join(os.path.splitext(params['fasta'])[:-1])
-    params['out_dir'] = base_dir
-  if not os.path.isdir(base_dir):
-    os.makedirs(base_dir)
-
-  if not dict_get(params, 'csv'):
-    basename = '.'.join(os.path.splitext(params['fasta'])[:-1])
-    params['csv'] = basename + '.csv'
-  params['csv'] = os.path.abspath(params['csv'])
-
-  params['citations'] = os.path.join(params['out_dir'], 'citations.txt')
-  params['citations'] = os.path.abspath(params['citations'])
-  
-  fasta = "input.fasta"
-  shutil.copy(params['fasta'], os.path.join(base_dir, fasta))
-  params['fasta'] = fasta
+    """
+    Creates a directory for all output files and makes it the current
+    working directory. copies the input sequences into it as 'input.fasta'.
+    """
+    from helpers import dict_get
 
-  shutil.copy(os.path.join(os.getcwd(), 'inmembrane.config'), base_dir)
+    if dict_get(params, 'out_dir'):
+        base_dir = params['out_dir']
+    else:
+        base_dir = '.'.join(os.path.splitext(params['fasta'])[:-1])
+        params['out_dir'] = base_dir
+    if not os.path.isdir(base_dir):
+        os.makedirs(base_dir)
 
-  os.chdir(base_dir)
+    if not dict_get(params, 'csv'):
+        basename = '.'.join(os.path.splitext(params['fasta'])[:-1])
+        params['csv'] = basename + '.csv'
+    params['csv'] = os.path.abspath(params['csv'])
+
+    params['citations'] = os.path.join(params['out_dir'], 'citations.txt')
+    params['citations'] = os.path.abspath(params['citations'])
+
+    fasta = "input.fasta"
+    shutil.copy(params['fasta'], os.path.join(base_dir, fasta))
+    params['fasta'] = fasta
+
+    shutil.copy(os.path.join(os.getcwd(), 'inmembrane.config'), base_dir)
+
+    os.chdir(base_dir)
 
 
 def import_protocol_python(params):
-  """
-  Some python magic that loads the desired protocol file
-  encoded in the string 'params['protocol'] as a python file
-  with the internal variable name 'protocol'. An appropriate
-  python command is generated that is to be processed by
-  the 'exec' function.
-  """
-  protocol_py = os.path.join(module_dir, 'protocols', params['protocol']+'.py')
-  if not os.path.isfile(protocol_py):
-    raise IOError("Couldn't find protcols/" + protocol_py)
-  return 'import inmembrane.protocols.%s as protocol' % (params['protocol'])
+    """
+    Some python magic that loads the desired protocol file
+    encoded in the string 'params['protocol'] as a python file
+    with the internal variable name 'protocol'. An appropriate
+    python command is generated that is to be processed by
+    the 'exec' function.
+    """
+    protocol_py = os.path.join(module_dir, 'protocols',
+                               params['protocol'] + '.py')
+    if not os.path.isfile(protocol_py):
+        raise IOError("Couldn't find protcols/" + protocol_py)
+    return 'import inmembrane.protocols.%s as protocol' % (params['protocol'])
 
 
 def process(params):
-  """
-  Main program loop. Triggers the 'protocol' found in the params
-  to annotate all proteins give the list of annotations needed by
-  'protocol'. Then outputs to screen and a .csv file.
-  """
-  from helpers import dict_get, create_proteins_dict, log_stdout, log_stderr
-  # will load all plugins in the plugins/ directory
-  from inmembrane.plugins import *
-
-  # initializations
-  exec(import_protocol_python(params))
-  init_output_dir(params)
-  seqids, proteins = create_proteins_dict(params['fasta'])
-
-  # TODO: ideally this loop needs to be run within the protocol,
-  #       since for some protocols not all plugins
-  #       will be run for every sequence, conditional
-  #       on the outcome of a previous analysis
-  #       eg. protocol.run(params, proteins)
-
-  # annotates with external binaries as found in plugins
-  for plugin_str in protocol.get_annotations(params):
-    plugin = eval(plugin_str)
-    plugin.annotate(params, proteins)
-  
-  # do protocol analysis on the results of the annotations
-  for seqid in seqids:
-    protein = proteins[seqid]
-    protocol.post_process_protein(params, protein)
-    log_stdout(protocol.protein_output_line(seqid, proteins))
-
-  # print a summary table of classifications to stderr
-  log_stderr(protocol.summary_table(params, proteins))
-
-  # always write to biologist-friendly csv file
-  f = open(params['csv'], 'w')
-  for seqid in seqids:
-    f.write(protocol.protein_csv_line(seqid, proteins))
-  f.close()
-  log_stderr("\n")
-  log_stderr("Output written to %s" % (params['csv']))
-
-  # TODO: citations for specific HMMs (PFAM etc ?)
-  
-  # write citations to a file and gracefully deal with plugins
-  # without a citation defined
-  import codecs
-  import textwrap
-  f = codecs.open(params['citations'], mode='w', encoding='utf-8')
-  programs_used = []
-  for program in protocol.get_annotations(params):
-    plugin = eval(program)
-    try:
-      f.write(plugin.citation['name']+":\n")
-      f.write(textwrap.fill(plugin.citation['ref']))
-    except AttributeError:
-      f.write("%s - no citation provided." % program)
-    f.write("\n\n")
-    try:
-      programs_used.append(plugin.citation['name'])
-    except (AttributeError, KeyError):
-      programs_used.append(program)
-    
-  f.close()
-  log_stderr("\n")
-  log_stderr("This run used %s." % (", ".join(programs_used)) )
-  log_stderr("References have been written to %s \n"
-             "# - please cite as appropriate." % 
-             (params['citations']) )
-             
-  return proteins
+    """
+    Main program loop. Triggers the 'protocol' found in the params
+    to annotate all proteins give the list of annotations needed by
+    'protocol'. Then outputs to screen and a .csv file.
+    """
+    from helpers import dict_get, create_proteins_dict, log_stdout, log_stderr
+    # will load all plugins in the plugins/ directory
+    from inmembrane.plugins import *
+
+    # initializations
+    exec (import_protocol_python(params))
+    init_output_dir(params)
+    seqids, proteins = create_proteins_dict(params['fasta'])
+
+    # TODO: ideally this loop needs to be run within the protocol,
+    #       since for some protocols not all plugins
+    #       will be run for every sequence, conditional
+    #       on the outcome of a previous analysis
+    #       eg. protocol.run(params, proteins)
+
+    # annotates with external binaries as found in plugins
+    for plugin_str in protocol.get_annotations(params):
+        plugin = eval(plugin_str)
+        plugin.annotate(params, proteins)
+
+    # do protocol analysis on the results of the annotations
+    for seqid in seqids:
+        protein = proteins[seqid]
+        protocol.post_process_protein(params, protein)
+        log_stdout(protocol.protein_output_line(seqid, proteins))
+
+    # print a summary table of classifications to stderr
+    log_stderr(protocol.summary_table(params, proteins))
+
+    # always write to biologist-friendly csv file
+    f = open(params['csv'], 'w')
+    for seqid in seqids:
+        f.write(protocol.protein_csv_line(seqid, proteins))
+    f.close()
+    log_stderr("\n")
+    log_stderr("Output written to %s" % (params['csv']))
+
+    # TODO: citations for specific HMMs (PFAM etc ?)
+
+    # write citations to a file and gracefully deal with plugins
+    # without a citation defined
+    import codecs
+    import textwrap
+    f = codecs.open(params['citations'], mode='w', encoding='utf-8')
+    programs_used = []
+    for program in protocol.get_annotations(params):
+        plugin = eval(program)
+        try:
+            f.write(plugin.citation['name'] + ":\n")
+            f.write(textwrap.fill(plugin.citation['ref']))
+        except AttributeError:
+            f.write("%s - no citation provided." % program)
+        f.write("\n\n")
+        try:
+            programs_used.append(plugin.citation['name'])
+        except (AttributeError, KeyError):
+            programs_used.append(program)
+
+    f.close()
+    log_stderr("\n")
+    log_stderr("This run used %s." % (", ".join(programs_used)))
+    log_stderr("References have been written to %s \n"
+               "# - please cite as appropriate." %
+               (params['citations']))
+
+    return proteins

inmembrane/helpers.py

@@ -67,7 +67,7 @@ def silence_log(b):
     LOG_SILENT = b
 
 
-def log_stderr(s):
+def log_stderr(s, width=76, comment=True):
     """
     Wrapper for all stderr out. Allows future customization.
     """
@@ -80,9 +80,9 @@ def log_stderr(s):
     sys.stderr.write(s)
 
 
-def log_stdout(s):
+def log_stdout(s, width=76):
     """
-    Wrapper for all stderr out. Allows future customization.
+    Wrapper for all stdout output. Allows future customization.
     """
     if LOG_SILENT:
         return

inmembrane/plugins/__init__.py

@@ -6,4 +6,4 @@
 
 __all__ = []
 for p in pkgutil.iter_modules(__path__):
-  __all__.append(p[1])
+    __all__.append(p[1])