Mercurial > repos > pieterlukasse > prims_metabolomics2

changeset 21:43902da5d00e

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changed match_library location again
author linda.bakker@wur.nl <linda.bakker@wur.nl>
date Wed, 06 May 2015 08:06:53 +0200
parents f70b2c169e3a
children f0c6feab06e7
files GCMS/library_lookup.xml GCMS/match_library.py match_library.py
diffstat 3 files changed, 134 insertions(+), 134 deletions(-) [+]
line wrap: on
line diff
--- a/GCMS/library_lookup.xml	Fri May 01 14:08:26 2015 +0200
+++ b/GCMS/library_lookup.xml	Wed May 06 08:06:53 2015 +0200
@@ -61,7 +61,7 @@
   <outputs>
     <data format="tabular" label="${tool.name} on" name="output" />
 </outputs>
-<code file="match_library.py" />
+<code file="../match_library.py" />
   <help>
 Performs a lookup of the RI values by matching CAS numbers from the given NIST identifications file to a library.
 If a direct match is NOT found for the preferred column name, a regression can be done to find
--- a/GCMS/match_library.py	Fri May 01 14:08:26 2015 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-'''
-Containing functions are called from Galaxy to populate lists/checkboxes with selectable items
-'''
-import csv
-import glob
-import os
-
-
-__author__ = "Marcel Kempenaar"
-__contact__ = "brs@nbic.nl"
-__copyright__ = "Copyright, 2012, Netherlands Bioinformatics Centre"
-__license__ = "MIT"
-
-def get_column_type(library_file):
-    '''
-    Returns a Galaxy formatted list of tuples containing all possibilities for the
-    GC-column types. Used by the library_lookup.xml tool
-    @param library_file: given library file from which the list of GC-column types is extracted
-    '''
-    if library_file == "":
-        galaxy_output = [("", "", False)]
-    else:
-        (data, header) = read_library(library_file)
-    
-        if 'columntype' not in header:
-            raise IOError('(get_column_type) Missing columns in  ', library_file)
-    
-        # Filter data on column type
-        column_type = header.index("columntype")
-        amounts_in_list_dict = count_occurrence([row[column_type] for row in data])
-        galaxy_output = [(str(a) + "(" + str(b) + ")", a, False) for a, b in amounts_in_list_dict.items()]
-        
-    return(galaxy_output)
-
-
-def filter_column(library_file, column_type_name):
-    '''
-    Filters the Retention Index database on column type
-    @param library_file: file containing the database
-    @param column_type_name: column type to filter on
-    '''
-    if library_file == "":
-        galaxy_output = [("", "", False)]
-    else:
-        (data, header) = read_library(library_file)
-    
-        if ('columntype' not in header or
-            'columnphasetype' not in header):
-            raise IOError('(filter_column) Missing columns in ', library_file)
-    
-        column_type = header.index("columntype")
-        statphase = header.index("columnphasetype")
-    
-        # Filter data on colunn type name
-        statphase_list = [line[statphase] for line in data if line[column_type] == column_type_name]
-        amounts_in_list_dict = count_occurrence(statphase_list)
-        galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()]
-        
-    return(sorted(galaxy_output))
-
-
-def filter_column2(library_file, column_type_name, statphase):
-    '''
-    Filters the Retention Index database on column type
-    @param library_file: file containing the database
-    @param column_type_name: column type to filter on
-    @param statphase: stationary phase of the column to filter on
-    '''
-    if library_file == "":
-        galaxy_output = [("", "", False)]
-    else:
-        (data, header) = read_library(library_file)
-    
-        if ('columntype' not in header or
-            'columnphasetype' not in header or
-            'columnname' not in header):
-            raise IOError('(filter_column2) Missing columns in ', library_file)
-    
-        column_type_column = header.index("columntype")
-        statphase_column = header.index("columnphasetype")
-        column_name_column = header.index("columnname")
-    
-        # Filter data on given column type name and stationary phase
-        statphase_list = [line[column_name_column] for line in data if line[column_type_column] == column_type_name and
-                          line[statphase_column] == statphase]
-        amounts_in_list_dict = count_occurrence(statphase_list)
-        galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()]
-        
-    return(sorted(galaxy_output))
-
-
-def read_library(filename):
-    '''
-    Reads a CSV file and returns its contents and a normalized header
-    @param filename: file to read
-    '''
-    data = list(csv.reader(open(filename, 'rU'), delimiter='\t'))
-    header_clean = [i.lower().strip().replace(".", "").replace("%", "") for i in data.pop(0)]
-    return(data, header_clean)
-
-
-
-def get_directory_files(dir_name):
-    '''
-    Reads the directory and
-    returns the list of .txt files found as a dictionary
-    with file name and full path so that it can 
-    fill a Galaxy drop-down combo box.
-    
-    '''
-    files = glob.glob(dir_name + "/*.*")
-    if len(files) == 0:
-        # Configuration error: no library files found in <galaxy-home-dir>/" + dir_name :
-        galaxy_output = [("Configuration error: expected file not found in <galaxy-home-dir>/" + dir_name, "", False)]
-    else:
-        galaxy_output = [(str(get_file_name_no_ext(file_name)), str(os.path.abspath(file_name)), False) for file_name in files]
-    return(galaxy_output)
-    
-def get_file_name_no_ext(full_name):
-    '''
-    returns just the last part of the name
-    '''
-    simple_name = os.path.basename(full_name)
-    base, ext = os.path.splitext(simple_name)
-    return base
-    
-
-def count_occurrence(data_list):
-    '''
-    Counts occurrences in a list and returns a dict with item:occurrence
-    @param data_list: list to count items from
-    '''
-    return dict((key, data_list.count(key)) for key in set(data_list))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/match_library.py	Wed May 06 08:06:53 2015 +0200
@@ -0,0 +1,133 @@
+'''
+Containing functions are called from Galaxy to populate lists/checkboxes with selectable items
+'''
+import csv
+import glob
+import os
+
+
+__author__ = "Marcel Kempenaar"
+__contact__ = "brs@nbic.nl"
+__copyright__ = "Copyright, 2012, Netherlands Bioinformatics Centre"
+__license__ = "MIT"
+
+def get_column_type(library_file):
+    '''
+    Returns a Galaxy formatted list of tuples containing all possibilities for the
+    GC-column types. Used by the library_lookup.xml tool
+    @param library_file: given library file from which the list of GC-column types is extracted
+    '''
+    if library_file == "":
+        galaxy_output = [("", "", False)]
+    else:
+        (data, header) = read_library(library_file)
+    
+        if 'columntype' not in header:
+            raise IOError('(get_column_type) Missing columns in  ', library_file)
+    
+        # Filter data on column type
+        column_type = header.index("columntype")
+        amounts_in_list_dict = count_occurrence([row[column_type] for row in data])
+        galaxy_output = [(str(a) + "(" + str(b) + ")", a, False) for a, b in amounts_in_list_dict.items()]
+        
+    return(galaxy_output)
+
+
+def filter_column(library_file, column_type_name):
+    '''
+    Filters the Retention Index database on column type
+    @param library_file: file containing the database
+    @param column_type_name: column type to filter on
+    '''
+    if library_file == "":
+        galaxy_output = [("", "", False)]
+    else:
+        (data, header) = read_library(library_file)
+    
+        if ('columntype' not in header or
+            'columnphasetype' not in header):
+            raise IOError('(filter_column) Missing columns in ', library_file)
+    
+        column_type = header.index("columntype")
+        statphase = header.index("columnphasetype")
+    
+        # Filter data on colunn type name
+        statphase_list = [line[statphase] for line in data if line[column_type] == column_type_name]
+        amounts_in_list_dict = count_occurrence(statphase_list)
+        galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()]
+        
+    return(sorted(galaxy_output))
+
+
+def filter_column2(library_file, column_type_name, statphase):
+    '''
+    Filters the Retention Index database on column type
+    @param library_file: file containing the database
+    @param column_type_name: column type to filter on
+    @param statphase: stationary phase of the column to filter on
+    '''
+    if library_file == "":
+        galaxy_output = [("", "", False)]
+    else:
+        (data, header) = read_library(library_file)
+    
+        if ('columntype' not in header or
+            'columnphasetype' not in header or
+            'columnname' not in header):
+            raise IOError('(filter_column2) Missing columns in ', library_file)
+    
+        column_type_column = header.index("columntype")
+        statphase_column = header.index("columnphasetype")
+        column_name_column = header.index("columnname")
+    
+        # Filter data on given column type name and stationary phase
+        statphase_list = [line[column_name_column] for line in data if line[column_type_column] == column_type_name and
+                          line[statphase_column] == statphase]
+        amounts_in_list_dict = count_occurrence(statphase_list)
+        galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()]
+        
+    return(sorted(galaxy_output))
+
+
+def read_library(filename):
+    '''
+    Reads a CSV file and returns its contents and a normalized header
+    @param filename: file to read
+    '''
+    data = list(csv.reader(open(filename, 'rU'), delimiter='\t'))
+    header_clean = [i.lower().strip().replace(".", "").replace("%", "") for i in data.pop(0)]
+    return(data, header_clean)
+
+
+
+def get_directory_files(dir_name):
+    '''
+    Reads the directory and
+    returns the list of .txt files found as a dictionary
+    with file name and full path so that it can 
+    fill a Galaxy drop-down combo box.
+    
+    '''
+    files = glob.glob(dir_name + "/*.*")
+    if len(files) == 0:
+        # Configuration error: no library files found in <galaxy-home-dir>/" + dir_name :
+        galaxy_output = [("Configuration error: expected file not found in <galaxy-home-dir>/" + dir_name, "", False)]
+    else:
+        galaxy_output = [(str(get_file_name_no_ext(file_name)), str(os.path.abspath(file_name)), False) for file_name in files]
+    return(galaxy_output)
+    
+def get_file_name_no_ext(full_name):
+    '''
+    returns just the last part of the name
+    '''
+    simple_name = os.path.basename(full_name)
+    base, ext = os.path.splitext(simple_name)
+    return base
+    
+
+def count_occurrence(data_list):
+    '''
+    Counts occurrences in a list and returns a dict with item:occurrence
+    @param data_list: list to count items from
+    '''
+    return dict((key, data_list.count(key)) for key in set(data_list))