diff format_input_selector.py @ 0:e7cd19afda2e draft

Lefse

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/format_input_selector.py	Tue May 13 21:57:00 2014 -0400
@@ -0,0 +1,77 @@
+from galaxy import datatypes,model
+import sys,string,time
+
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+def get_opt(data):
+	return [('r','r',False),('c','c',False)]
+
+def red(st,l):
+	if len(st) <= l: return st 
+	l1,l2 = l/2,l/2
+	return st[:l1]+".."+st[len(st)-l2:]
+
+def get_row_names(data,t):
+	if data == "": return []
+	max_len =38                 
+	fname = data.dataset.file_name
+	opt = []
+	rc = ''
+#	lines = [(red(v.split()[0],max_len),'%s' % str(v.split()[0]),False) for i,v in enumerate(open(fname))]
+	if t == 'b': lines = [(red(v.split()[0],max_len),'%d' % (i+1),False) for i,v in enumerate(open(fname)) if len(v.split()) > 3 ] 
+	else: lines = [(red(v.split()[0],max_len),'%d' % (i+1),False) for i,v in enumerate(open(fname))]
+	return sorted(opt+lines)
+
+def get_cols(data,t,c):
+	if data == "": return []
+	max_len =32 
+	fname = data.dataset.file_name
+	opt = []
+	if c != 'cl':
+		opt.append(('no '+c,'%d' % -1,False))
+	if t == 'c': 
+		rc = ''
+		lines = [(red((rc+"#"+str(i+1)+":"+v[0]),max_len),'%d' % (i+1),False) for i,v in enumerate(zip(*[line.split() for line in open(fname)]))]
+	else:
+		rc = ''
+		lines = [(red((rc+"#"+str(i+1)+":"+v.split()[0]),max_len),'%d' % (i+1),False) for i,v in enumerate(open(fname))]
+	return opt+lines
+
+"""
+def get_phecols(i,addNone,hint):
+   hint = hint.lower()
+   fname = i.dataset.file_name
+   try:
+        f = open(fname,'r')
+   except:
+        return [('get_phecols unable to open file "%s"' % fname,'None',False),]
+   header = f.next()
+   h = header.strip().split()
+   dat = [(x,'%d' % i,False) for i,x in enumerate(h)]
+   matches = [i for i,x in enumerate(h) if x.lower().find(hint) <> -1]
+   if len(matches) > 0:
+       sel = matches[0]
+       dat[sel] = (dat[sel][0],dat[sel][1],True)
+   if addNone:
+        dat.insert(0,('None - no Manhattan plot','0', False ))
+   return dat
+"""
+
+
+"""
+def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
+    outfile = 'out_html'
+    job_name = param_dict.get( 'name', 'Manhattan QQ plots' )
+    killme = string.punctuation + string.whitespace
+    trantab = string.maketrans(killme,'_'*len(killme))
+    newname = '%s.html' % job_name.translate(trantab)
+    data = out_data[outfile]
+    data.name = newname
+    data.info='%s run at %s' % (job_name,timenow())
+    out_data[outfile] = data
+    app.model.context.flush()
+"""