def get_geneids_from_affy(affy_id_list, affy_file=None):
"""
Returns a dictionary mapping affy probe ids to
the tuple (genebank,unigene,symbol) given an input list
of affy probe ids, and a csv file from affymetrix with
the appropriate information
@param affy_id_list: A list of strings like '1000_at'...
@param affy_file: If none, then the function get_affy_key_file()
will be called to get the full file name and path to the csv file,
else specify the filename/path.
"""
if affy_file is None:
affy_file = get_affy_key_file()
affy_dict = {}
lines = []
with open(affy_file, "r") as f:
for tmpline in f:
if tmpline[0] != "#":
lines.append(tmpline) # omit header/comment lines
for i, ln in enumerate(lines[1:]): # lines[0] is the column headers
ifr.print_progress(i, len(lines))
tmp = ifr.smart_split(ln, sep=",")
key = tmp[0]
genebank = tmp[8]
unigene = tmp[10]
symbol = tmp[14]
affy_dict[key] = (genebank, unigene, symbol)
return affy_dict
def gen_affy_to_geneId_dict(affy_file_subdir="HG_U95A.na33.annot", affy_fn="HG_U95A.na33.annot.csv"):
"""
Converts a list of affymetric probe set ids into a genelist
with names suitable for querying gather or kegg. Generates
a dictionary with entries { affy_id : gene_id_list }. Most times, gene_id_list will
have only a single entry, but several probes have multiple Gene IDs given.
@param affy_file_subdir: The subdirectory of the ifr.DATA_DIR that has
the HG_U95A.na33.annot.csv file.
@param affy_fn: The csv file in the subdirectory with the data. The parameter is
provided in case the file was renamed from the orginal name of "HG_U95A.na33.annot.csv"
@note: Relies on a data file called HG_U95A.na33.annot.csv that must be present
in the HG_U95A.na33.annot subdirectory of the linked Data directory. It would
be most efficient to use this function once and save the resulting dictionary
in a pickle file for later use instead of having to re-parse the data.
"""
affy_dict = {}
affy_file = os.path.join(ifr.DATA_DIR, affy_file_subdir, affy_fn)
lines = []
with open(affy_file, "r") as f:
for tmpline in f:
if tmpline[0] != "#":
lines.append(tmpline) # omit header/comment lines
for i, ln in enumerate(lines[1:]): # lines[0] is the column headers
ifr.print_progress(i, len(lines))
tmp = ifr.smart_split(ln, sep=",")
key = tmp[0]
val = tmp[14]
if val == "---":
# this affy id has no gene symbol
genelist = []
elif "///" in val: # there are more than one GeneIds for this probe
# print "Subfield indicator in Gene Symbol for %s, line: %d."%(key,(i+1))
# print "Val: %s"%tmp[14]
genelist = [x.strip() for x in val.split("///") if x.strip() != ""]
else:
genelist = [val]
affy_dict[key] = list(set(genelist)) # remove duplicates
return affy_dict
