# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1426767266 -3600
# Node ID f70b775dcaa56c3f0a41e8387ac69b56069448f3
# Parent  2f98ba53f30813b14a1f260d54eb33cbb10bfdbc
removed redundant match_lib

diff -r 2f98ba53f308 -r f70b775dcaa5 metaMS/match_library.py
--- a/metaMS/match_library.py	Thu Mar 19 12:35:32 2015 +0100
+++ /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('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('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('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))