def main_common( filename,option='select_genes' ):
global current_outputdir
cod = current_outputdir
img_select_genes = 'dumy' # required for menu_template.htm
img_cluster_genes = 'dummy' # required for menu_template.htm
img_cluster_tissues = 'dummy' # required for menu_template.htm
if option=='select_genes': img_select_genes = 'img'
if option=='cluster_genes': img_cluster_genes = 'img'
if option=='cluster_tissues': img_cluster_tissues = 'img'
if option=='select_genes':
program = 'all'
else:
program = option
option_formatted = option.replace("_"," ").title()
menus = \
"""
<font size="2" face="Arial">
<p> <a href="conf_select_data?program=%(program)s&filter=*.dat&initial_file=%(filename)s">Specify</a> data file. (Currently %(filename)s)</p>
<p> <a href="conf_select_genes">Set options for %(option_formatted)s</a></p>
<p> <a href="conf_select_outputdir">Specify output directory</a>.
(Currently %(cod)s )
</p>
<p>
<form method="post" action="/run">
<input type="hidden" name="select_genes" value="1" />
<input type="submit" value="GO"/>
</form>
</p>
<p> <a href="/review">Review</a> results</p>
</font>
""" % locals()
menus = menus.replace('select_genes', option)
return webutil.apply_template('menu_template.htm', locals(), globals())
def review_corr_thumbnails(directory, REQUEST):
"Reviews the thumbnails of the correlation coefficients"
def check_display(file):
return file.endswith(".cor")
body = _thumbnails(directory,check_display)
URL0 = "Correlation Thumbnails"
return webutil.apply_template('review_sub.htm', locals(), globals())
def review_data_thumbnails(directory, REQUEST):
"""Reviews all the heatmaps in a directory in a thumbnail format"""
def check_display(file):
description, show_heatmap = _file_info(file)
return show_heatmap
body = _thumbnails(directory,check_display)
URL0 = "Thumbnails"
return webutil.apply_template('review_sub.htm', locals(), globals())
def display_running_processes():
"Returns a list of what's running"
list = []
for program_name, data_file, stdin_file, stdout_file in \
EmmixProcessManager.listRunningProcesses():
list.append( """
<tr>
<td><a href="display_info?stdout=%s">%s</a></td>
<td>%s</td>
</tr>
""" % (stdout_file,program_name, data_file))
body = "".join(list)
return webutil.apply_template('running.htm', locals(), globals())
def review_sstats(filename, REQUEST):
"Reviews the sstats file for a given filename"
results, URL0 = _getEmmixResult(filename)
datafile = results.data_filename
result_dir = results.result_dirname
html="""
Edit the gene descriptions <a href="/edit_gene_info?datafile=%s&result_dir=%s">here</a>.
""" % (datafile, result_dir)
html+="""
<table>
<tr>
<!--<th>n-th selected gene</th>-->
<th>log-lambda</th>
<th>minimum cluster size</th>
<th>original gene number</th>
<th>gene description</th>
</tr>
"""
try:
for line in open(filename,'r').readlines():
selected_gene_number, loglambda, minsample, gene_number = \
filter(lambda x: x, line.split(' '))
html+='''
<tr>
<!-- <td align="right">%s</td> -->
<td align="right">%s</td>
<td align="right">%s</td>
<td align="right">%s</td>''' \
% (selected_gene_number, loglambda, minsample, gene_number)
gene=results.getSelectedGene(int(selected_gene_number))
if gene:
html+='<td>%s</td></tr>\n' % gene.description
else:
html+='<td>No description found</td></tr>\n'
html+='</table></html>'
body=html
except TypeError:
# Hmm, sstats has less than 4 columns
body='<pre>%s</pre>' % open(filename,'r').read()
return webutil.apply_template('review_sub.htm', locals(), globals())
def review(directory=None,REQUEST=None):
"""Review the results"""
if not directory:
outputdir=open(CURRENT_OUTPUTDIR_PATH).read()
outputdir=outputdir.split('results\\')[1]
REQUEST.response.redirect(REQUEST.URL + '/%s/' % outputdir)
return
#
# Work out a path into a directory
#
traverse_subpath = REQUEST.traverse_subpath
path = os.path.join( *[RESULT_PATH, directory] + traverse_subpath)
REQUEST['path']=path
relative_path=os.path.join( * ([directory] + traverse_subpath) )
# If correlation files need to be computed then
# do it now
if os.path.isdir(path):
emmixgene.calculateCorrelationForDirectory(path)
else:
emmixgene.calculateCorrelationForDirectory(os.path.dirname(path))
# if file is an image, let the image module
# handle it
#
extension=os.path.splitext(path.lower())[1]
if extension in (".png",".svg"):
return _heatmap(path, REQUEST)
# if file is sstats, then use EmmixResult class
# help in the display
if path.lower().endswith('.sstats') or \
path.lower().endswith('.stats'):
return review_sstats(path, REQUEST)
if path.lower().find(".dat.cut_list") >= 0 :
return review_list(path, REQUEST)
#
# if file exists, set mime type and return the file
# otherwise, return a directory listing
#
if os.path.isfile(path):
REQUEST.response.setHeader("Mime-Type","text/html")
body='<pre>%s</pre>' % open(path,"rb").read()
URL0=os.path.basename(path)
return webutil.apply_template('review_sub.htm', locals(), globals())
elif os.path.isdir(path):
if not REQUEST.URL.endswith('/'):
REQUEST.response.setBase(REQUEST.URL+"/")
else:
# path is not a file and not a directory
# try and make it a directory
print "xxx making directory " , path, extension
recurse_mkdir(path)
#
# directory listing
#
files = os.listdir(path)
import numsort
files = numsort.sorted_copy(files)
output = ""
review_correlations = ""
for file in files:
if file.endswith(".cor") and not review_correlations:
# allow people to review correlation heatmaps
# if .cor files exist
review_correlations = """<p>View correlation coefficients <a href="/review_corr_thumbnails?directory=%s">as thumbnails</a> </p>""" % relative_path
description, show_heatmap = _file_info(file)
if (description != "" and show_heatmap != 0):
# generate heatmaps for these
output += '''
<a href="%(file)s">%(file)s</a> <b>%(description)s</b>
<a href="%(file)s.png" title="png format">[heatmap]</a>
<a href="%(file)s.svg" title="svg format">[heatmap]</a><br/>
''' % locals()
elif (description !="" and show_heatmap == 0):
# only display the file
output += '<a href="%s">%s</a> <b>%s</b> <br/>' % \
(file, file, description)
files = os.listdir("results")
other_directories = ""
for file in files:
dir_path = os.path.join("results",file)
if os.path.isdir(dir_path):
other_directories += '<a href="../%s/">%s</a><br/>\n' % (file, file)
body = """
<h1>Review results</h1>
<h2>You are reviewing: %(path)s</h2>
<p>View heatmaps
<a href="/review_data_thumbnails?directory=%(relative_path)s">as thumbnails</a>
</p>
%(review_correlations)s
%(output)s
<p><a href="file://%(path)s" target="_blank">Open</a> the current results folder</p>
<hr/>
<H2>
Review results in other directories
</H2>
%(other_directories)s
<hr/>
<b>Note the following is a mock up only</b>
<h2>Logs</h2>
<font size="-1">
<TABLE>
<TR>
<TD>Data File
</TD>
<TD>Anon.dat
</TD>
</TR>
<TR>
<TD>Date run
</TD>
<TD>15/10/2001
</TD>
</TR>
<TR>
<TD>Researcher Notes
</TD>
<TD>ddd
</TD>
</TR>
<TR>
<TD>%(path)s
</TD>
<TD>
</TD>
</TR>
</TABLE>
</font>
<hr/>
""" % webutil._multimap(globals(), locals())
return webutil.apply_template('review.htm', locals(), globals())
def conf_cluster_tissues(REQUEST):
"""Screen to configure cluster tissue parameters"""
if REQUEST['REQUEST_METHOD']=="POST":
#
# By default limit the number of rows
# unless specified
#
limit_rows=1
if REQUEST.has_key('limit_rows'):
if REQUEST['limit_rows']=='0':
limit_rows=0
for key in current_rule.params_cluster_tissues.keys():
if REQUEST.has_key(key):
if key == 'num_rows' and not limit_rows:
current_rule.params_cluster_tissues['num_rows']=0
elif REQUEST[key]:
current_rule.params_cluster_tissues[key]=REQUEST[key]
current_rule.params_cluster_tissues['use_factor_analyzers']=\
getattr(REQUEST, 'use_factor_analyzers', 0)
current_rule.store_rule(CURRENT_RULE_PATH)
REQUEST.response.redirect("/main_cluster_tissues")
return ""
option_formatted = """
<a href="/main_cluster_tissues">Cluster Tissues</a> > Options
"""
img_select_genes = "dummy"
img_cluster_genes = "dummy"
img_cluster_tissues = "img"
html = """
<h2>Options for cluster-tissues</h2>
<form action="" method="post">
Use factor analyzers
<input type="checkbox"
oldvalue="%(use_factor_analyzers)s"
name="use_factor_analyzers"
value="1"/><br/>
Number of factors (only used with factor analyzers)
<input type="text"
name="num_factors:int"
value="%(num_factors)s"><br/>
Number of components
<input type="text"
name="num_components:int"
value="%(num_components)s"><br/>
Random starts
<input type="text"
name="random_starts:int"
value="%(random_starts)s"><br/>
K-Mean starts
<input type="text"
name="kmean_starts:int"
value="%(kmean_starts)s"><br/>
Random seed 1
<input type="text"
name="random_seed1:int"
value="%(random_seed1)s"><br/>
Random seed 2
<input type="text"
name="random_seed2:int"
value="%(random_seed2)s"><br/>
Random seed 3
<input type="text"
name="random_seed3:int"
value="%(random_seed3)s"><br/>
<!-- ============== limit number of rows computed ============== -->
<input type="radio" id="limit_rows" name="limit_rows" value="1">Limit rows
<input type="radio" id="all_rows" name="limit_rows" value="0"/>
Use all rows<br/>
Number of rows to use (from top of file)
<input type="text" name="num_rows" value="%(num_rows)s"><br/>
<p>
<input type="button" value="Restore to default"><BR/>
<input type="submit" value="OK">
<input type="submit" value="Cancel">
</p>
""" % current_rule.params_cluster_tissues
html = html.replace('oldvalue="1"', 'checked')
if current_rule.params_cluster_tissues['num_rows']:
html = html.replace('id="limit_rows"','checked')
else:
html = html.replace('id="all_rows"','checked')
menus = html
return webutil.apply_template('menu_template.htm',locals(), globals())
def conf_cluster_genes(REQUEST):
"""Web screen to configure Cluster Genes parameters"""
if REQUEST['REQUEST_METHOD']=="POST":
#
# By default limit the number of rows
# unless specified
#
limit_rows=1
if REQUEST.has_key('limit_rows'):
if REQUEST['limit_rows']=='0':
limit_rows=0
for key in current_rule.params_cluster_genes.keys():
if REQUEST.has_key(key):
if key == 'num_rows' and not limit_rows:
current_rule.params_cluster_genes['num_rows']=0
elif REQUEST[key]:
current_rule.params_cluster_genes[key]=REQUEST[key]
for key in ['robust', 'reorder']:
if not REQUEST.has_key(key):
current_rule.params_cluster_genes[key]="no"
current_rule.store_rule(CURRENT_RULE_PATH)
REQUEST.response.redirect("/main_cluster_genes")
return ""
option_formatted = """
<a href="/main_cluster_genes">Cluster Genes</a> > Configure
"""
img_select_genes = "dummy"
img_cluster_genes = "img"
img_cluster_tissues = "dummy"
html = """
<h2>Options to run cluster-genes with</h2>
<form action="" method="post">
Random starts <input type="text" name="random_starts"
value="%(random_starts)s"><br/>
K-Mean starts <input type="text" name="kmean_starts"
value="%(kmean_starts)s"><br/>
Random starts spherical <input type="text" name="random_starts_spherical"
value="%(random_starts_spherical)s"><br/>
K-Mean starts spherical <input type="text" name="kmean_starts_spherical"
value="%(kmean_starts_spherical)s"><br/>
Number of groups to cluster <input type="text" name="cluster_groups"
value="%(cluster_groups)s"><br/>
Threshold cluster size <input type="text" name="threshold_clustersize"
value="%(threshold_clustersize)s"><br/>
Random seed 1 <input type="text" name="random_seed1"
value="%(random_seed1)s"><br/>
Random seed 2 <input type="text" name="random_seed2"
value="%(random_seed2)s"><br/>
Random seed 3 <input type="text" name="random_seed3"
value="%(random_seed3)s"><br/>
Reorder tissues <input type="checkbox" name="reorder"
id="reorder" value="yes" oldvalue="%(reorder)s"> <br/>
Robust <input type="checkbox" name="robust"
id="robust" value="yes" oldvalue="%(robust)s"> <br/>
Common value of nu <input type="text" name="nu"
value="%(nu)s"> (robust version only) <br/>
<!-- ============== limit number of rows computed ============== -->
<input type="radio" id="limit_rows" name="limit_rows" value="1">Limit rows
<input type="radio" id="all_rows" name="limit_rows" value="0"/>
Use all rows<br/>
Number of rows to use (from top of file)
<input type="text" name="num_rows" value="%(num_rows)s"><br/>
<input type="button" value="Restore to default"><BR/>
<input type="submit" value="OK">
<input type="submit" value="Cancel">
</p>
""" % current_rule.params_cluster_genes
if current_rule.params_cluster_genes['num_rows']:
html = html.replace('id="limit_rows"','checked')
else:
html = html.replace('id="all_rows"','checked')
#
# replace checkboxes values
#
html = html.replace('oldvalue="yes"', 'checked')
menus = html
return webutil.apply_template('menu_template.htm',locals(), globals())
def conf_select_genes(REQUEST):
"""Screen to configure select genes parameters"""
global current_rule
if REQUEST['REQUEST_METHOD']=="POST":
#
# By default limit the number of rows
# unless specified
#
limit_rows=1
if REQUEST.has_key('limit_rows'):
if REQUEST['limit_rows']=='0':
limit_rows=0
for key in current_rule.params_select_genes.keys():
if REQUEST.has_key(key):
if key == 'num_rows' and not limit_rows:
current_rule.params_select_genes['num_rows']=0
elif REQUEST[key]:
current_rule.params_select_genes[key]=REQUEST[key]
for key in ['resume']:
if not REQUEST.has_key(key):
current_rule.params_select_genes[key]=0
current_rule.store_rule(CURRENT_RULE_PATH)
REQUEST.response.redirect("/main_select_genes")
return ""
option_formatted = """
<a href="/main_select_genes">Select Genes</a> > Options
"""
img_select_genes = "img"
img_cluster_genes = "dummy"
img_cluster_tissues = "dummy"
html = """
<h2>Options to run select-genes with</h2>
<form action="" method="post">
<table>
<tr>
<td>Random starts</td>
<td><input type="text" name="random_starts" value="%(random_starts)s"></td>
</tr>
<tr>
<td>K-Mean starts</td>
<td><input type="text" name="kmean_starts" value="%(kmean_starts)s"></td>
</tr>
<tr>
<td>Random seed 1</td>
<td><input type="text" name="random_seed1" value="%(random_seed1)s"></td>
</tr>
<tr>
<td>Random seed 2</td>
<td><input type="text" name="random_seed2" value="%(random_seed2)s"></td>
</tr>
<tr>
<td>Random seed 3</td>
<td><input type="text" name="random_seed3" value="%(random_seed3)s"></td>
</tr>
<tr>
<td>Threshold likelihood</td>
<td><input type="text" name="threshold_likelihood"
value="%(threshold_likelihood)s"></td>
</tr>
<tr>
<td>Threshold cluster size</td>
<td><input type="text" name="threshold_clustersize"
value="%(threshold_clustersize)s"></td>
</tr>
<!-- ============== limit number of rows computed ============== -->
<tr>
<td colspan="2">
<input type="radio" id="limit_rows" name="limit_rows" value="1">Limit rows
<input type="radio" id="all_rows" name="limit_rows" value="0"/>
Use all rows
</td>
</tr>
<tr>
<td>Number of rows to use (from top of file)</td>
<td><input type="text" name="num_rows" value="%(num_rows)s"></td>
</tr>
<!-- ============= resume past calculation ===================== -->
<tr>
<td colspan="2">
<input type="checkbox"
name="resume:int"
value="1"
checked="%(resume)s">If unfinished job exists, resume unfinished job.
</td>
</tr>
<tr colspan="2">
<td><input type="button" value="Restore to default"></td>
</tr>
<tr colspan="2">
<td>
<input type="submit" value="OK">
<input type="submit" value="Cancel">
</td>
</tr>
</table>
""" % current_rule.params_select_genes
if current_rule.params_select_genes['num_rows']:
html = html.replace('id="limit_rows"','checked')
else:
html = html.replace('id="all_rows"','checked')
html = html.replace('checked="0"', '')
menus = html
return webutil.apply_template('menu_template.htm',locals(), globals())
def index_html(REQUEST, RESPONSE):
"Obligatory doc_string"
msgs.restore('messages.txt')
messages=msgs.displayMessages()
select_genes_filename=current_datafiles.select_genes.filename
cluster_genes_filename=current_datafiles.cluster_genes.filename
cluster_tissues_filename=current_datafiles.cluster_tissues.filename
RESPONSE.setHeader("Expires","-1")
RESPONSE.setHeader("Cache-Control", "no-cache")
RESPONSE.setHeader("Pragma", "no-cache")
if messages:
messages="""
<h3>Messages</h3>
<table bgcolor="#cccc99" border="0">
<tr>
<td>
%(messages)s
</td>
</tr>
<tr align="right">
<td>
<a href="/msgs/deleteAllMessages">Delete all messages</a>
</td>
</tr>
</table>
""" % locals()
return webutil.apply_template('default.htm', locals(), globals())
html ="""
%(standard_html_header)s
<H2>Main menu</H2>
<table valign="top">
<tr valign="top">
<td valign="top">
<p>
<a href="/main_select_genes">Select-genes</a>
</p>
<p>
<a href="/main_cluster_genes">Cluster-genes</a>
</p>
<p>
<a href="/main_cluster_tissues">Cluster-tissues</a>
</p>
</td>
<td>
<h3>Running processes</h3>
<table bgcolor="#cccc99" border="0">
<tr>
<td>
%(runningProcesses)s
</td>
</tr>
</table>
<!-- **************** MESSAGES ************* -->
%(messages)s
<p>
<a href="/reportBack">Create an error report</a> for Chui</a>
</p>
</td>
</tr>
</table>
<hr/>
<H2>Help</H2>
<p><b>select-genes</b> uses the emmix algorithm to reduce a large dataset
of genes to a smaller set which is subsequently used for clustering.</p>
<p><b>cluster-genes</b> clusters commonly expressed genes into groups.</p>
<p><b>cluster-tissues</b> ... </p>
%(standard_html_footer)s
""" % _multimap(locals(), globals())
return html % _multimap(locals(), globals())