Mercurial > repos > simon-gladman > degust

diff degust.py @ 1:773107d91822 draft

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author simon-gladman
date Mon, 24 Feb 2014 00:41:33 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/degust.py	Mon Feb 24 00:41:33 2014 -0500
@@ -0,0 +1,178 @@
+#!/usr/bin/env python
+
+import argparse, json, re, sys, csv, StringIO, math
+
+def embed(csv, args):
+    html="""
+<html>
+  <head profile="http://www.w3.org/2005/10/profile">
+    <link rel="icon" type="image/png" href="images/favicon.png"/>
+
+    <!-- Externals CSS -->
+    <link rel="stylesheet" href='http://victorian-bioinformatics-consortium.github.io/degust/dist/latest/css/lib.css' />
+
+    <link rel="stylesheet" href='http://victorian-bioinformatics-consortium.github.io/degust/dist/latest/css/common.css' type="text/css" />
+    <link rel="stylesheet" href='http://victorian-bioinformatics-consortium.github.io/degust/dist/latest/css/compare.css' type="text/css "/>
+
+    <script type="text/javascript" src='http://victorian-bioinformatics-consortium.github.io/degust/dist/latest/common.js'></script>
+    <script type="text/javascript" src='http://victorian-bioinformatics-consortium.github.io/degust/dist/latest/slickgrid.js'></script>
+    <script type="text/javascript" src='http://victorian-bioinformatics-consortium.github.io/degust/dist/latest/compare.js'></script>
+  </head>
+  <body>
+    <div id="replace-me" class="container">
+      <div class="jumbotron">
+        <h1>Degust</h1>
+        <p><a href='http://victorian-bioinformatics-consortium.github.io/degust/'>Degust</a> is preparing your data...  prepare for degustation...</p>
+        <img src='http://victorian-bioinformatics-consortium.github.io/degust/dist/latest/images/front-loader.gif'>
+      </div>
+    </div>
+
+    <script type="text/javascript">
+      window.settings = { };
+    </script>
+  </body>
+</html>
+
+         """
+    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))
+