GEO / GPLRaw Data에서 GSM정보 추출하기

Input file: GPL1440_family.tar.gz
Output file: parsing_gsm_relation.txt, parsing_gsm_err.txt, parsing_gsm_results.txt

 

import glob
import gzip

## Reading GPL Files
files_gpl = glob.glob('./GPLRaw/*.soft.gz')

## Recording parsing results
files_result = open('parsing_GSM_results.txt', 'w')

## Recording Relation GPL, GSE, GSM
files_relation = open('parsing_GSM_relation.txt', 'w')

## Recording parsing errors
files_err = open('parsing_GSM_err.txt', 'w')
str_err = ''

def splicing_line(line):
	tmp = line.split('=')
	arr = []
	if(tmp[0].startswith('!')):
		_tmp = tmp[0].lstrip('!')
		arr.append(_tmp.strip())
	else:
		arr.append(tmp[0].strip())

	arr.append(tmp[1].strip())
	return arr


for afile in files_gpl:

	gpl_name = afile.replace('./GPLRaw/', '')
	gpl_name = gpl_name.rstrip('_family.soft.gz')

	print afile
	line_err = ''
	# Opening a gzip file
	
	file_gz = gzip.open(afile)

	# Extracting lines for SAMPLE
	sample_name = ''

	flag_sample_start = False

	for line in file_gz:
		#print line
		try:
			line_err = line
			if(line.startswith('^SAMPLE')):
				flag_sample_start = True
				arr = line.split('=')
				sample_name = arr[1].strip()
	
				#arr = splicing_line(line)
	
			if(line.startswith('!sample_table_begin')):
				flag_sample_start = False
	
			if(line.startswith('!sample_table_end')):
				flag_sample_start = False
	
			if(flag_sample_start):
				if(line.startswith('!')):
					arr = splicing_line(line)
					files_result.write(sample_name + '\t' + arr[0] + '\t' + arr[1] + '\n')
					if(line.startswith('!Sample_series_id')):
						arr = splicing_line(line)
						files_relation.write(gpl_name + '\t' + arr[1] + '\t' +sample_name + '\n')

		except Exception, e:
			print "Error", line.strip(), '%s' % e
			files_err.write(line.strip() + '\t' + '%s' % e + '\n')

	file_gz.close()

	# Break for Test
	#break

files_err.close()
files_relation.close()
files_result.close()