Mercurial > repos > peterjc > venn_list

comparison tools/plotting/venn_list.py @ 4:29fcd027d67a draft

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Uploaded v0.0.6 take 1, simple test (which currently fails)
author peterjc
date Thu, 16 May 2013 12:43:57 -0400
parents aefc86eda5f6
children
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3:bacb7dfa846c 4:29fcd027d67a
3 3
4 This script is copyright 2010 by Peter Cock, The James Hutton Institute 4 This script is copyright 2010 by Peter Cock, The James Hutton Institute
5 (formerly SCRI), UK. All rights reserved. 5 (formerly SCRI), UK. All rights reserved.
6 See accompanying text file for licence details (MIT/BSD style). 6 See accompanying text file for licence details (MIT/BSD style).
7 7
8 This is version 0.0.3 of the script. 8 This is version 0.0.4 of the script.
9 """ 9 """
10 10
11 11
12 import sys 12 import sys
13 import rpy 13 import rpy
44 print "Doing %i-way Venn Diagram" % n 44 print "Doing %i-way Venn Diagram" % n
45 45
46 def load_ids(filename, filetype): 46 def load_ids(filename, filetype):
47 if filetype=="tabular": 47 if filetype=="tabular":
48 for line in open(filename): 48 for line in open(filename):
49 if not line.startswith("#"): 49 line = line.rstrip("\n")
50 yield line.rstrip("\n").split("\t",1)[0] 50 if line and not line.startswith("#"):
51 yield line.split("\t",1)[0]
51 elif filetype=="fasta": 52 elif filetype=="fasta":
52 for line in open(filename): 53 for line in open(filename):
53 if line.startswith(">"): 54 if line.startswith(">"):
54 yield line[1:].rstrip("\n").split(None,1)[0] 55 yield line[1:].rstrip("\n").split(None,1)[0]
55 elif filetype.startswith("fastq"): 56 elif filetype.startswith("fastq"):