Mercurial > repos > peterjc > venn_list
view tools/plotting/venn_list.py @ 2:c96bef0643dc draft
Uploaded v0.0.3 again to revert upload of wrong file. Sigh.
author | peterjc |
---|---|
date | Mon, 06 May 2013 14:05:13 -0400 |
parents | baf7031d470e |
children | 6aae6bc0802d |
line wrap: on
line source
#!/usr/bin/env python """Plot up to 3-way Venn Diagram using R limma vennDiagram (via rpy) This script is copyright 2010 by Peter Cock, The James Hutton Institute (formerly SCRI), UK. All rights reserved. See accompanying text file for licence details (MIT/BSD style). This is version 0.0.3 of the script. """ import sys import rpy def stop_err(msg, error_level=1): """Print error message to stdout and quit with given error level.""" sys.stderr.write("%s\n" % msg) sys.exit(error_level) try: import rpy except ImportError: stop_err("Requires the Python library rpy (to call R)") try: rpy.r.library("limma") except: stop_err("Requires the R library limma (for vennDiagram function)") if len(sys.argv)-1 not in [7, 10, 13]: stop_err("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv)-1)) all_file, all_type, all_label = sys.argv[1:4] set_data = [] if len(sys.argv)-1 >= 7: set_data.append(tuple(sys.argv[4:7])) if len(sys.argv)-1 >= 10: set_data.append(tuple(sys.argv[7:10])) if len(sys.argv)-1 >= 13: set_data.append(tuple(sys.argv[10:13])) pdf_file = sys.argv[-1] n = len(set_data) print "Doing %i-way Venn Diagram" % n def load_ids(filename, filetype): if filetype=="tabular": for line in open(filename): if not line.startswith("#"): yield line.rstrip("\n").split("\t",1)[0] elif filetype=="fasta": for line in open(filename): if line.startswith(">"): yield line[1:].rstrip("\n").split(None,1)[0] elif filetype.startswith("fastq"): #Use the Galaxy library not Biopython to cope with CS from galaxy_utils.sequence.fastq import fastqReader handle = open(filename, "rU") for record in fastqReader(handle): #The [1:] is because the fastaReader leaves the @ on the identifer. yield record.identifier.split()[0][1:] handle.close() elif filetype=="sff": try: from Bio.SeqIO import index except ImportError: stop_err("Require Biopython 1.54 or later (to read SFF files)") #This will read the SFF index block if present (very fast) for name in index(filename, "sff"): yield name else: stop_err("Unexpected file type %s" % filetype) def load_ids_whitelist(filename, filetype, whitelist): for name in load_ids(filename, filetype): if name in whitelist: yield name else: stop_err("Unexpected ID %s in %s file %s" % (name, filetype, filename)) if all_file in ["", "-", '""', '"-"']: #Load without white list sets = [set(load_ids(f,t)) for (f,t,c) in set_data] #Take union all = set() for s in sets: all.update(s) print "Inferred total of %i IDs" % len(all) else: all = set(load_ids(all_file, all_type)) print "Total of %i IDs" % len(all) sets = [set(load_ids_whitelist(f,t,all)) for (f,t,c) in set_data] for s, (f,t,c) in zip(sets, set_data): print "%i in %s" % (len(s), c) #Now call R library to draw simple Venn diagram try: #Create dummy Venn diagram counts object for three groups cols = 'c("%s")' % '","'.join("Set%i" % (i+1) for i in range(n)) rpy.r('groups <- cbind(%s)' % ','.join(['1']*n)) rpy.r('colnames(groups) <- %s' % cols) rpy.r('vc <- vennCounts(groups)') #Populate the 2^n classes with real counts #Don't make any assumptions about the class order #print rpy.r('vc') for index, row in enumerate(rpy.r('vc[,%s]' % cols)): if isinstance(row, int) or isinstance(row, float): #Hack for rpy being too clever for single element row row = [row] names = all for wanted, s in zip(row, sets): if wanted: names = names.intersection(s) else: names = names.difference(s) rpy.r('vc[%i,"Counts"] <- %i' % (index+1, len(names))) #print rpy.r('vc') if n == 1: #Single circle, don't need to add (Total XXX) line names = [c for (t,f,c) in set_data] else: names = ["%s\n(Total %i)" % (c, len(s)) for s, (f,t,c) in zip(sets, set_data)] rpy.r.assign("names", names) rpy.r.assign("colors", ["red","green","blue"][:n]) rpy.r.pdf(pdf_file, 8, 8) rpy.r("""vennDiagram(vc, include="both", names=names, main="%s", sub="(Total %i)", circle.col=colors) """ % (all_label, len(all))) rpy.r.dev_off() except Exception, exc: stop_err( "%s" %str( exc ) ) rpy.r.quit( save="no" ) print "Done"