Degust is preparing your data... prepare for degustation...
+
+
+
+
+
+
+
+
+ """
+ enc = json.dumps(csv)
+ columns = \
+ ["{idx:%s, name: %s, type:'info'}"%(json.dumps(c),json.dumps(c)) for c in args.info] + \
+ ["{idx:%s, name: 'FDR', type: 'fdr'}"%json.dumps(args.fdr)] + \
+ ["{idx:%s, name: 'Average', type: 'avg'}"%json.dumps(args.avg)] + \
+ ["{idx:%s, name: %s, type: 'primary'}"%(json.dumps(args.primary), json.dumps(args.primary))] + \
+ ["{idx:%s, name: %s, type:'fc'}"%(json.dumps(c),json.dumps(c)) for c in args.logFC] + \
+ ["{idx:%s, name: %s, type:'link'}"%(json.dumps(c),json.dumps(c)) for c in args.link_col]
+
+ settings = ["html_version: '0.11.2'",
+ "asset_base: 'http://victorian-bioinformatics-consortium.github.io/degust/dist/latest/'",
+ "csv_data: data",
+ "csv_format: %s"%("false" if args.tab else "true"),
+ "name: %s"%json.dumps(args.name),
+ "columns:[%s]"%(",".join(columns)),
+ ]
+ if args.notour:
+ settings += ["show_tour: false"]
+ if args.link_url:
+ settings += ["link_url: %s"%json.dumps(args.link_url)]
+
+ window_settings = "window.settings = {%s};"%(",".join(settings))
+ s = html.replace('window.settings = { };', "var data=%s;\n\n%s"%(enc,window_settings), 1)
+ return s
+
+def check_args(args, csv_file):
+ # Check args match csv file.
+ delim = "\t" if args.tab else ","
+ reader = csv.reader(csv_file.split('\n'), delimiter=delim)
+ headers = reader.next()
+ err = False
+ if args.avg is None:
+ sys.stderr.write("ERROR: Column for average expression not defined (use --avg) necessary for the ma-plot\n")
+ err=True
+ elif args.avg not in headers:
+ sys.stderr.write("ERROR: Column for average expression not found (%s)\n"%args.avg)
+ err=True
+
+ if args.fdr not in headers:
+ sys.stderr.write("ERROR: Column for FDR not found (%s)\n"%args.fdr)
+ err=True
+
+ if args.logFC is None:
+ sys.stderr.write("ERROR: No columns defined for log-fold-change, --logFC\n")
+ err=True
+ else:
+ for f in args.logFC:
+ if f not in headers:
+ sys.stderr.write("ERROR: Column for logFC not found, --logFC : (%s)\n"%f)
+ err=True
+
+ if args.info is None:
+ sys.stderr.write("ERROR: No columns defined for per-gene information, eg. gene IDs (use --info)\n")
+ err=True
+ else:
+ for f in args.info:
+ if f not in headers:
+ sys.stderr.write("ERROR: Column for info not found (%s)\n"%f)
+ err=True
+ return err
+
+
+def cuffdiff_avg(str):
+ """Given a string that is the output from cuffdiff, create and log2(average expression) column.
+ Acutally, it is just the average log2() of the FPKM, but that should be enough for visualisation
+ """
+ delim = "\t" if args.tab else ","
+ reader = csv.reader(csv_file.split('\n'), delimiter=delim)
+ si = StringIO.StringIO()
+ cw = csv.writer(si, delimiter=delim)
+
+ headers = reader.next()
+ cw.writerow(headers + ['Avg'])
+ idx1 = headers.index("value_1")
+ idx2 = headers.index("value_2")
+ tst_idx = headers.index("status")
+ for r in reader:
+ if len(r)>=max(idx1,idx2) and r[tst_idx] == 'OK':
+ v1 = max(float(r[idx1]),1)
+ v2 = max(float(r[idx2]),1)
+ v = 0.5 * (math.log(v1,2) + math.log(v2,2))
+ cw.writerow(r + [v])
+ return si.getvalue()
+
+parser = argparse.ArgumentParser(description='Produce a standalone Degust html file from a CSV file containing DGE.')
+parser.add_argument('csvfile', type=argparse.FileType('r'),
+ nargs='?', default='-',
+ help="CSV file to process (default stdin)")
+parser.add_argument('-o','--out', type=argparse.FileType('w'),
+ default='-',
+ help="Output file (default stdout)")
+
+parser.add_argument('--name', default='Unnamed',
+ help='Name for this DGE comparison')
+parser.add_argument('--notour',
+ help='Do not show the tour on first load')
+parser.add_argument('--primary', default='pri',
+ help='Name for the primary condition that the fold-changes are relative to')
+parser.add_argument('--avg',
+ help='Name for average intensity column in CSV file')
+parser.add_argument('--fdr', default='adj.P.Val',
+ help='Name for "FDR" column in CSV file (default "adj.P.Val")')
+parser.add_argument('--logFC',
+ help='Comma separated names for "logFC" columns in CSV file')
+parser.add_argument('--info',
+ help='Comma separated names for info columns in CSV file')
+parser.add_argument('--link-col',
+ help='Name for column to use with "--link-url"')
+parser.add_argument('--link-url',
+ help='Gene info URL. Used when double-clicking the gene-table. Any "%%s" will be replaced with the value from the specified "--link-col"')
+parser.add_argument('--tab', action='store_true', default=False,
+ help='Specify that the csv file is actually tab delimited')
+parser.add_argument('--cuffdiff', action='store_true', default=False,
+ help='Input file is from cuffdiff (gene_exp.diff). This will set the columns automatically. Note this is still experimental')
+
+args = parser.parse_args()
+
+#print args
+if args.info: args.info = args.info.split(",")
+if args.logFC: args.logFC = args.logFC.split(",")
+args.link_col = [args.link_col] if args.link_col else []
+
+# print args
+
+if args.csvfile == sys.stdin:
+ sys.stderr.write("Reading from stdin...\n")
+
+csv_file = args.csvfile.read()
+
+if args.cuffdiff:
+ args.info = ['gene_id','gene']
+ args.logFC = ['log2(fold_change)']
+ args.tab = True
+ args.fdr = 'q_value'
+ args.avg = 'Avg'
+ csv_file = cuffdiff_avg(csv_file)
+
+err = check_args(args, csv_file)
+
+if not err:
+ args.out.write(embed(csv_file, args))
+
+