Mercurial > repos > mkh > ips5

diff interproscan5/create_html_index.py @ 3:74cf3f49f10c draft
Better HTML index.
author: mkh
date: Tue, 02 Feb 2016 12:27:19 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interproscan5/create_html_index.py	Tue Feb 02 12:27:19 2016 -0500
@@ -0,0 +1,112 @@
+#!/usr/bin/env python
+
+import os
+import re
+import sys
+
+START = '''<html>
+<head>
+<style>
+    a:link { text-decoration: none; color: red; }
+    a:visited { text-decoration: none; color: blue; }
+    a:hover { text-decoration: underline; color: green; } a:active { text-decoration: underline; color: green; }
+</style>
+</head>
+<body>
+<h1>InterProScan result summary page</h1>
+'''
+
+END = '''
+</body>
+</html>
+'''
+
+
+def raw_mode(html_file, directory):
+    with open(html_file, 'w') as h:
+        h.write(START)
+        h.write('<ul>')
+        for filename in [f for f in sorted(os.listdir(directory)) if os.path.isfile(os.path.join(directory, f))]:
+            h.write('<li><a href="%s"> %s </a></li>' % (filename, os.path.splitext(filename)[0]))
+        h.write('</ul>')
+        h.write(END)
+
+
+def fix_name(name):
+    return re.sub('[&/]', '_', name)
+
+
+def cooked_mode(orfed_ids, tsv_file, html_file, directory):
+    name_freq = {}
+    with open(tsv_file) as f:
+        for line in f:
+            name = line.split("\t", 1)[0]
+            if orfed_ids:
+                deorfed_name = re.sub('_\\d+$', '', name)
+            else:
+                deorfed_name = name
+
+            data = name_freq.get(deorfed_name, [])
+            if data:
+                data[0] += 1
+                data[1][name] = data[1].get(name, 0) + 1
+            else:
+                data = [1, {name: 1}]
+            name_freq[deorfed_name] = data
+
+    name_freq_sorted = [(x[0], (x[1][0], sorted(x[1][1].items(), key=lambda t: t[1], reverse=True)))
+                        for x in sorted(name_freq.items(), key=lambda t: t[1][0], reverse=True)
+                        ]
+
+    filename_dict = {}
+    for filename in [f for f in os.listdir(directory) if os.path.isfile(os.path.join(directory, f))]:
+        filename_dict[os.path.splitext(filename)[0]] = filename
+
+    with open(html_file, 'w') as h:
+        h.write(START)
+        h.write('<ol>')
+        for don, (freq, members) in name_freq_sorted:
+            h.write('\n<li>')
+            if len(members) == 1:
+                fn = fix_name(members[0][0])
+                if fn in filename_dict:
+                    h.write('<a href="%s"> %s (%d features)</a>' %
+                            (filename_dict[fn], members[0][0], members[0][1]))
+                    del filename_dict[fn]
+                else:
+                    h.write('<a href="%s"> %s (%d features, broken link!)</a>' %
+                            (members[0][0], members[0][0], members[0][1]))
+            else:
+                h.write('%s (%d features)' % (don, freq))
+                h.write('\n<ul>')
+                for n, f in members:
+                    fn = fix_name(n)
+                    if fn in filename_dict:
+                        h.write('\n<li><a href="%s"> %s (%d features)</a></li>' % (filename_dict[fn], n, f))
+                        del filename_dict[fn]
+                    else:
+                        h.write('\n<li><a href="%s"> %s (%d features, broken link!)</a></li>' % (n, n, f))
+                h.write('</ul>')
+            h.write('</li>')
+
+        if len(filename_dict) > 0:
+            h.write('<h2>Sequences without any features</h2>')
+            h.write('\n<ul>')
+            for n, p in sorted(filename_dict.items(), key=lambda t: t[0]):
+                h.write('\n<li><a href="%s">%s</li>' % (p, n))
+            h.write('</ul>')
+        h.write('</ol>')
+        h.write(END)
+
+
+def main():
+    if len(sys.argv) == 3:
+        raw_mode(sys.argv[1], sys.argv[2])
+    elif len(sys.argv) == 5:
+        cooked_mode(sys.argv[1] != '0', sys.argv[2], sys.argv[3], sys.argv[4])
+    else:
+        print('Args must be "html_file directory" or "[0|1] tsv_file html_file directory"')
+        sys.exit(1)
+
+
+main()