On 26/06/14 09:18, Myunggyo Lee wrote:
Hi all
I just started to learn python language.
Welcome.
I'm trying to figure out the reason of error but i couldn't find it.
first imports short.txt(is attached to this mail)
and read in dictionary named gpdic1
Others have pointed out the specific problems with your code.
However you general approach could be different too using some of
Pythons features.
# -*- coding: utf-8 -*-
import string, os, sys, time, glob
You should not need to import string any more.
It is a remnant of very old Python code. Its functionality
is (almost) all in the built-in string objects nowadays.
Especially if you are using python v3 - which you don't
tell us...
inf2 =open('short.txt','r')
gpdic1={}
while 1:
line= inf2.readline()
if not line: break
A better way of doing this in Python is to use a
for loop.
You could rewrite the lines above as one line:
for line in open('short.txt'): # 'r' is the default mode
lines = line[:-1].split(',')
rather than stripping of the lst character its usually better to use the
rstrip() method - there migfht be more than one character to be removed...
lines = line.rstrip().split(',')
Also if this is a comma separated file, as seems to be implied by the
split(). You will find a csv module in the standard library that can
make this much easier. It can read the data directly from the file
into a list of dictionaries via a DictReader object.
hgene = lines[1]
chr1 = lines[4]
hgstart = lines[5]
hgstop = lines[6]
tgene = lines[7]
chr2 = lines[10]
tgstart = lines[11]
tgstop = lines[12]
gpdic1["hgene"] = hgene
gpdic1["chr1"] = chr1
gpdic1["hgstart"] = hgstart
gpdic1["hgstop"] = hgstop
gpdic1["tgene"] = tgene
gpdic1["chr2"] = chr2
gpdic1["tgstart"] = tgstart
gpdic1["tgstop"] = tgstop
You could have done all of that directly and avoided the double assignments.
ie
gpdic1["hgene"] = lines[1]
etc...
The csv.DictReader would do it all for you and correctly
return a list of dicts instead of just the last one.
import csv
datafile = open(...)
data = csv.DictReader(datafile)
data is now a collection of dictionaries each of
which is like your gpdic1 above.
If the file does not include the required keys in the
first line you can provide them as a list of strings
to DictReader - see the manual...
Python has a wealth of modules in its library and part of
becoming a good Python programmer is in learning whats
there and how to use it. That takes time and experience
but its often a quick Google in case.
Finally, it looks a lot like bioscience. There are some
specific Python modules (and versions) designed for
that area. You may find a Google search for Python and
bioscience throws up something useful.
hth
--
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
http://www.flickr.com/photos/alangauldphotos
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