[ANN] basereader

[Maurice LING]

The following codes had been donated to the BioPython project.

--------------------
"""
A simple script to read BASE (BioArray Software Environment) non-serial
result output file format.
Outputs five global lists: FileHead, SectionRegister, SpotSectionInfo,
SpotRegisterInfo and SpotRegisterIntensity.
FileHead contains the first line of the file.
SectionRegister contains the 3rd line of the file to the next blank
line. It typically contains the file information section.
SpotSectionInfo contains the next section (which is the spot section)
after the file information section, without the actual spots data.
SpotRegisterInfo contains all the information of the spots in the file.
SpotRegisterIntensity contains only the intensity values of the spots
(corresponding to each row on the SpotRegisterInfo).

This script is written by Maurice HT LING, The University of Melbourne,
under the sponsorship of the Cooperative Research Centre for Innovative
Dairy Products.
Copyright 2004 Maurice HT Ling
"""
import sys
import string

global SectionRegister
global FileHead
global SpotSectionInfo
global SpotRegisterInfo, SpotRegisterIntensity
SectionRegister = []
FileHead = []
SpotSectionInfo = []
SpotRegister = []
SpotRegisterIntensity = []

def BaseReader(file):
"""Reads the entire file and append the data into the specified lists.
base = open(file)

# reads 1st line of line (supposed to be "BASEfile") and
# puts it in FileHead as a list
str = base.readline()
FileHead.append(str)
str = base.readline()

# reads 1st section (supposed to be information section),
# until it hits a blank line
while (str != '\n'):
#print str
str = string.split(str, '\t')
SectionRegister.append(str)
str = base.readline()

# gets through the blank line
str = base.readline()

# reads information portion of 2nd section (supposed to be spots section)
# until it hit "%"
str = base.readline()
while (str != '%\n'):
str = string.split(str, '\t')
SpotSectionInfo.append(str)
str = base.readline()

# reads spots data, puts everything into SpotRegister
# extracts intensity values into SpotRegisterIntensity
str = base.readline()
while (str):
str = string.split(str, '\t')
SpotRegister.append(str)
SpotRegisterIntensity.append(str[-2:])
str = base.readline()

#close the file
base.close()

def SpotIntensityToFloat(list):
"""A method to convert the SpotRegisterIntensity list from string into
float values.
t = []
for s in list:
a = [float(s[0]), float(s[1])]
t.append(a)
return t


--
Maurice Han Tong LING, BSc(Hons), Adv Dip Comp
mobile: +61 4 22781753
+65 96669233
mailing address: Department of Zoology, The University of Melbourne
Royal Parade, Parkville, Victoria 3010, Australia
residential address: 1/44 Gatehouse Street
Parkville, Victoria 3053, Australia
email: (e-mail address removed)
resume: http://maurice.vodien.com/maurice_resume.pdf
www: http://www.geocities.com/beldin79/

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