maldisoft/readsample.py

import os
import sys

class readsample:

	def __init__(self, file, hash_keys=None, delimeter=None, skip=2):
		"Open file and read the header."
		self.fd = open(file, "r")
		self.delimeter = delimeter
		self.hash_keys = hash_keys
		self.read_head(skip)
		pass

	def next(self):
		"Read one record of the file and hash the fields"
		line = self.fd.readline()
		
		if not line:
			return None
		if self.delimeter != None:
			result = line.split(delimeter)
		else:
			result = line.split()
		if self.hash_keys:
			return self.createHash(result, self.hash_keys)
		else:
			return [float(x) for x in result]


	def readAll(self):
		"Read all records and return a list"
		sample_list = []
		sample = self.next()
		while sample:	
			sample_list.append(sample)
			sample = self.next()

		return sample_list

	def read_head(self, skip = 2):
		"This is to remove the header of the file"
		"Reusing this code requires modifying this function"
		"Most times just skip lines, and just change the default skip number"

		for i in range(skip):	
			self.fd.readline()

	def createHash(self, s_line, hash_keys):
		"This is to create a hash with the fields of the record"
		"The record is already splitted in one list"
		hash_res = {}
		for i in range(len(hash_keys)):
			hash_res[hash_keys[i]] = float(s_line[i])   # want to improve this to tuples

		return hash_res


	def close(self):
		self.fd.close()


def main():
	"Main to test the library"
	samples = readsample(sys.argv[1], ["peak", "intensity"])

	value = samples.next() 
	while value:
		print value
		value = samples.next()

	samples.close()

	samples = readsample(sys.argv[2], None, None, 0)
	print samples.readAll()

if __name__ == '__main__':
	main()