diff tools/rgenetics/listFiles.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/listFiles.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,227 @@
+#Provides Upload tool with access to list of available files
+import glob,sys
+import galaxy.app as thisapp
+import galaxy.util
+
+from elementtree.ElementTree import XML
+
+librepos = '/usr/local/galaxy/data/rg'
+myrepos = '/home/rerla/galaxy'
+marchinirepos = '/usr/local/galaxy/data/rg/snptest'
+
+from galaxy.tools.parameters import DataToolParameter
+
+#Provides Upload tool with access to list of available builds
+
+builds = []
+#Read build names and keys from galaxy.util
+for dbkey, build_name in galaxy.util.dbnames:
+    builds.append((build_name,dbkey,False))
+
+#Return available builds
+def get_available_builds(defval='hg18'):
+    for i,x in enumerate(builds):
+        if x[1] == defval:
+           x = list(x)
+           x[2] = True
+           builds[i] = tuple(x)
+    return builds
+
+
+
+def get_tabular_cols( input, outformat='gg' ):
+    """numeric only other than rs for strict genome graphs
+    otherwise tabular. Derived from galaxy tool source around August 2007 by Ross"""
+    columns = []
+    seenCnames = {}
+    elems = []
+    colnames = ['Col%d' % x for x in range(input.metadata.columns+1)]
+    strict = (outformat=='gg')
+    for i, line in enumerate( file ( input.file_name ) ):
+        if line and not line.startswith( '#' ): 
+            line = line.rstrip('\r\n')
+            elems = line.split( '\t' )
+    
+            """
+            Strict gg note:
+            Since this tool requires users to select only those columns
+            that contain numerical values, we'll restrict the column select
+            list appropriately other than the first column which must be a marker
+            """
+            if len(elems) > 0:
+                for col in range(1, input.metadata.columns+1):
+		    isFloat = False # short circuit common result
+                    try:
+                        val = float(elems[col-1])
+                        isFloat = True
+                    except:
+                        val = elems[col-1]
+                        if val:
+                            if i == 0: # header row
+                               colnames[col] = val
+                    if isFloat or (not strict) or (col == 1): # all in if not GG
+                        option = colnames[col]
+                        if not seenCnames.get(option,None): # new
+                              columns.append((option,str(col),False))
+                              seenCnames[option] = option
+            #print 'get_tab: %d=%s. Columns=%s' % (i,line,str(columns))
+            if len(columns) > 0 and i > 10:
+                """
+                We have our select list built, so we can break out of the outer most for loop
+                """
+                break 
+        if i == 30:
+            break # Hopefully we never get here...
+    for option in range(min(5,len(columns))):
+      (x,y,z) = columns[option]
+      columns[option] = (x,y,True)
+    return columns # sorted select options
+
+def get_marchini_dir():
+    """return the filesystem directory for snptest style files"""
+    return marchinirepos
+
+
+def get_lib_SNPTESTCaCofiles():
+    """return a list of file names - without extensions - available for caco studies
+    These have a common file name with both _1 and _2 suffixes"""
+    d = get_marchini_dir()
+    testsuffix = '.gen_1' # glob these
+    flist = glob.glob('%s/*%s' % (d,testsuffix))
+    flist = [x.split(testsuffix)[0] for x in flist] # leaves with a list of file set names
+    if len(flist) > 0:
+        dat = [(flist[0],flist[0],True),]
+	dat += [(x,x,False) for x in flist[1:]]
+    else:
+        dat = [('No Marchini CaCo files found in %s - convert some using the Marchini converter tool' % d,'None',True),]
+    return dat
+
+def getChropt():
+    """return dynamic chromosome select options
+    """
+    c = ['X','Y']
+    c += ['%d' % x for x in range(1,23)]
+    dat = [(x,x,False) for x in c]
+    x,y,z = dat[3]
+    dat[3] = (x,y,True)
+    return dat
+
+
+def get_phecols(fname=''):
+   """ return a list of phenotype columns for a multi-select list
+   prototype:
+   foo = ('fake - not yet implemented','not implemented','False')
+   dat = [foo for x in range(5)]
+   return dat
+   """
+   try:
+   	header = file(fname,'r').next().split()
+   except:
+        return [('get_phecols unable to open file %s' % fname,'None',False),]
+   dat = [(x,x,False) for x in header]
+   return dat
+
+#Return various kinds of files
+
+def get_lib_pedfiles():
+    dat = glob.glob('%s/ped/*.ped' % librepos)
+    dat += glob.glob('%s/ped/*.ped' % myrepos)
+    dat.sort()
+    if len(dat) > 0:
+        dat = [x.split('.ped')[0] for x in dat]
+    	dat = [(x,x,'True') for x in dat]
+    else:
+        dat = [('No ped files - add some to %s/ped or %s/ped' % (librepos,myrepos),'None',True),]
+    return dat
+
+def get_lib_phefiles():
+    ext = 'phe'
+    dat = glob.glob('%s/pheno/*.%s' % (librepos,ext))
+    dat += glob.glob('%s/pheno/*.%s' % (myrepos,ext))
+    dat.sort()
+    if len(dat) > 0:
+    	dat = [(x,x,'False') for x in dat]
+    else:
+        dat = [('No %s files - add some to %s/pheno or %s/pheno' % (ext,librepos,myrepos),'None',True),]
+    return dat
+
+def get_lib_bedfiles():
+    dat = glob.glob('%s/plinkbed/*.bed' % librepos)
+    dat += glob.glob('%s/plinkbed/*.bed' % myrepos)
+    dat.sort()
+    if len(dat) > 0:
+        dat = [x.split('.bed')[0] for x in dat]
+    	dat = [(x,x,False) for x in dat]
+    else:
+        dat = [('No bed files - Please import some to %s/plinkbed or %s/plinkbed' % (librepos,myrepos),'None',True),]
+    return dat
+
+def get_lib_fbatfiles():
+    dat = glob.glob('%s/plinkfbat/*.ped' % librepos)
+    dat += glob.glob('%s/plinkfbat/*.ped' % myrepos)
+    dat.sort()
+    if len(dat) > 0:
+    	dat = [(x,x,False) for x in dat]
+    else:
+        dat = [('No fbat bed files - Please import some to %s/plinkfbat or %s/plinkfbat' % (librepos,myrepos),'None',True),]
+    return dat
+
+def get_lib_mapfiles():
+    dat = glob.glob('%s/ped/*.map' % librepos)
+    dat += glob.glob('%s/ped/*.map' % myrepos)
+    dat.sort()
+    if len(dat) > 0:
+    	dat = [(x,x,False) for x in dat]
+    else:
+        dat = [('No map files - add some to %s/ped' % librepos,'None',True),]
+    return dat
+
+def get_my_pedfiles():
+    dat = glob.glob('%s/*.ped' % myrepos)
+    if len(dat) > 0:
+    	dat = [(x,x,False) for x in dat]
+    else:
+        dat = [('No ped files - add some to %s' % librepos,'None',True),]
+    return dat
+
+def get_my_mapfiles():
+    dat = glob.glob('%s/*.map' % myrepos)
+    if len(dat) > 0:
+    	dat = [(x,x,'True') for x in dat]
+    else:
+        dat = [('No ped files - add some to %s' % librepos,'None',True),]
+    return dat
+
+def get_lib_xlsfiles():
+    dat = glob.glob('%s/*.xls' % librepos)
+    if len(dat) > 0:
+    	dat = [(x,x,False) for x in dat]
+    else:
+        dat = [('No ped files - add some to %s' % librepos,'None',True),]
+    return dat
+
+def get_lib_htmlfiles():
+    dat = glob.glob('%s/*.html' % librepos)
+    if len(dat) > 0:
+    	dat = [(x,x,False) for x in dat]
+    else:
+        dat = [('No ped files - add some to %s' % librepos,'None',True),]
+    return dat
+
+def get_my_xlsfiles():
+    dat = glob.glob('%s/*.xls' %  myrepos)
+    if len(dat) > 0:
+    	dat = [(x,x,False) for x in dat]
+    else:
+        dat = [('No ped files - add some to %s' % librepos,'None',True),]
+    return dat
+
+def get_my_htmlfiles():
+    dat = glob.glob('%s/*.html' % myrepos)
+    if len(dat) > 0:
+    	dat = [(x,x,False) for x in dat]
+    else:
+        dat = [('No ped files - add some to %s' % librepos,'None',True),]
+    return dat
+
+