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#!/usr/bin/env python
"""Parses Agilent Microarray output spreadsheet.
"""
from cogent.parse.record_finder import LabeledRecordFinder
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
def MicroarrayParser(lines):
"""Returns tuple: ([ProbeNames],[GeneNames],[LogRatios]) for all dots in
microarray file.
"""
probe_names = []
gene_names = []
log_ratios = []
#Make sure lines is not empty
if lines:
#Get the block of lines that starts with FEATURES
features_record = LabeledRecordFinder(\
lambda x: x.startswith('FEATURES'))
features_block = list(features_record(lines))
#Discard first block
features_block = features_block[1]
#Get the indices of GeneName and LogRatio from the block
features_list = features_block[0].split('\t')
probe_index = features_list.index('ProbeName')
gene_index = features_list.index('GeneName')
log_index = features_list.index('LogRatio')
#Get the lists for GeneName and LogRatio
for line in features_block[1:]:
temp = line.split('\t')
probe_names.append(temp[probe_index].upper())
gene_names.append(temp[gene_index].upper())
log_ratios.append(float(temp[log_index]))
return (probe_names, gene_names, log_ratios)
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