diff match_library.py @ 0:9d5f4f5f764b

Initial commit to toolshed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/match_library.py	Thu Jan 16 13:10:00 2014 +0100
@@ -0,0 +1,120 @@
+'''
+Containing functions are called from Galaxy to populate lists/checkboxes with selectable items
+'''
+import csv
+import glob
+import os
+
+
+__author__ = "Marcel Kempenaar"
+__contact__ = "[e-mail]"
+__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
+    '''
+    (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
+    '''
+    (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
+    '''
+    (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 + "/*.txt")
+    if len(files) == 0:
+        raise Exception("Configuration error: no library files found in <galaxy-home-dir>/" + dir_name)
+    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))