v2.1 Changes

README.md

@@ -15,19 +15,9 @@ You will need the following packages installed on your system:
 
 * Our pre-computed database, including instructions on how to create/upload the 
 database, can be found at ftp://supfam2.cs.bris.ac.uk/FATHMM/database
-* Create a configuration file named "config.ini" and enter the following (substituting 
-the required information with your credentials):
-
-```
-[DATABASE]
-HOST   = [MySQL Host]
-PORT   = [MySQL Port]
-USER   = [MySQL Username]
-PASSWD = [MySQL Password]
-DB     = fathmm
-```
-
-* Download "fathmm.py" from ./cgi-bin
+* Download "fathmm.py" and "config.ini" from the ./cgi-bin folder
+* Amend "config.ini", substituting the required information with your MySQL
+credentials:
 
 ## Running our Software
 
@@ -55,6 +45,8 @@ P43026 L441P
 P35555 N548I,E1073K,C2307S 
 ```
 
+## Optional Parameters
+
 The --help parameter can be used to view additional program parameters.  In brief,
 there are two optional parameters:
 
@@ -88,7 +80,4 @@ KW : UniProtKB KeyWords
 
 ## Known Issues:
 
-* Our predictions appear to be derived/written slower than previous version(s) of our 
-software - we are looking into this issue and will provide an update as soon as possible.
-
 We welcome any comments and/or suggestions that you may have regarding our software and server - please send an email directly to fathmm@biocompute.org.uk

cgi-bin/fathmm.py

@@ -167,7 +167,7 @@ def process_record(dbSNP, protein, substitution):
                 Tag = "DAMAGING" 
         else:
             # "Cancer-Associated" predictions ...
-            Tag = "NON-CANCER/PASSENGER"
+            Tag = "PASSENGER/OTHER"
 
             if float(Score) < -0.50:
                 Tag = "CANCER" 
@@ -217,13 +217,6 @@ def process_record(dbSNP, protein, substitution):
                       metavar = "<PHENO>",
                       default = "DO"
                       )
-    parser.add_option(
-                      "--HTML",
-                      dest = "HTML",
-                      help = SUPPRESS_HELP,
-                      action = "store_true",
-                      default = False
-                      ) # web-based parameter used to write HTML predictions - hidden from program user(s)
 
     (options, args) = parser.parse_args()
 
@@ -321,72 +314,3 @@ def process_record(dbSNP, protein, substitution):
 
     # move predictions to the requested location
     os.system("mv /tmp/" + os.path.basename(os.path.splitext(options.input)[0]) + ".tmp " + options.output)
-
-    # 
-    # WRITE WEB-BASED PREDICTIONS (IF REQUESTED)
-    #
-
-    if options.HTML:
-        HTM = open(os.path.splitext(options.output)[0] + ".htm", "w")
-        HTM.write(
-"""
-<table class="table table-striped">
-    <thead>
-        <tr>
-            <th>#</th>
-            <th>dbSNP ID</th>
-            <th>Protein ID</th>
-            <th>Substitution</th>
-            <th>Prediction</th>
-            <th>Score</th>
-            <th>Further Information</th>
-        </tr>
-    </thead>
-    <tbody>
-"""
-        )
-
-        for record in open(options.output, "r"):
-            if record and not record.startswith("#"):
-                record = record.split("\t")
-
-                # prediction formatting
-                if record[4] in [ "DAMAGING", "CANCER" ]:
-                    record[4] = "<p class='text-error'>%s</p>"% record[4]
-                else:
-                    record[4] = "<p class='text-success'>%s</p>"% record[4]
-
-                # warning/phenotypes formatting
-                if record[7].strip():
-                    record[6] = record[7]
-                else:
-                    if record[6].strip():
-                        record[6] = "<ul>" + "".join([ "<li>" + x + "</li>" for x in record[6].split("|") ]) + "</ul>"
-
-                HTM.write(
-"""
-        <tr>
-            <td>""" + record[0] + """</td>
-            <td>""" + record[1] + """</td>
-            <td>""" + record[2] + """</td>
-            <td>""" + record[3] + """</td>
-            <td>""" + record[4] + """</td>
-            <td>""" + record[5] + """</td>
-            <td>""" + record[6] + """</td>
-        </tr>
-"""
-        )
-
-        HTM.write(
-"""
-    </tbody>
-</table>
-
-<script>
-    document.getElementById("info").setAttribute("class", "btn btn-primary btn-large pull-right");
-    document.getElementById("info").innerHTML = "Download Predictions &raquo;";
-    
-    clearInterval(Refresh);
-</script>
-"""
-        )