diff rgWebLogo3.py @ 3:13045f6015cb draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 commit d0f167e74e705788adcd9c846db011aee490074b

--- a/rgWebLogo3.py	Fri Dec 18 19:20:26 2015 -0500
+++ b/rgWebLogo3.py	Fri Nov 17 09:38:19 2017 -0500
@@ -1,12 +1,17 @@
-"""
 # modified june 2 ross lazarus to add units option at Assaf Gordon's suggestion
 # rgWebLogo3.py
 # wrapper to check that all fasta files are same length
 
-"""
-import optparse, os, sys, subprocess, tempfile
+from __future__ import print_function
 
-WEBLOGO = 'weblogo' # executable name for weblogo3 - confusing isn't it?
+import optparse
+import os
+import subprocess
+import sys
+import tempfile
+
+WEBLOGO = 'weblogo'  # executable name for weblogo3 - confusing isn't it?
+
 
 class WL3:
     """
@@ -15,13 +20,13 @@
     FASTASTARTSYM = '>'
     badseq = '## error - sequences in file %s are not all the same length - cannot proceed. Please read the tool documentation carefully'
 
-    def __init__(self,opts=None):
-        assert opts<>None,'WL3 class needs opts passed in - got None'
+    def __init__(self, opts=None):
+        assert opts is not None, 'WL3 class needs opts passed in - got None'
         self.opts = opts
-        self.fastaf = file(self.opts.input,'r')
+        self.fastaf = open(self.opts.input, 'r')
         self.clparams = {}
 
-    def whereis(self,program):
+    def whereis(self, program):
         for path in os.environ.get('PATH', '').split(':'):
             if os.path.exists(os.path.join(path, program)) and not os.path.isdir(os.path.join(path, program)):
                 return os.path.join(path, program)
@@ -32,64 +37,62 @@
         """
         wl = self.whereis(WEBLOGO)
         if not wl:
-            print >> sys.stderr, '## rgWebLogo3.py error - cannot locate the weblogo binary %s on the current path' % WEBLOGO
-            print >> sys.stderr, '## Please ensure it is installed and working from http://code.google.com/p/weblogo'
+            print('## rgWebLogo3.py error - cannot locate the weblogo binary %s on the current path' % (WEBLOGO), file=sys.stderr)
+            print('## Please ensure it is installed and working from https://github.com/weblogo/weblogo', file=sys.stderr)
             sys.exit(1)
-        cll = [WEBLOGO,]
+        cll = [WEBLOGO, ]
         cll += [' '.join(it) for it in list(self.clparams.items())]
         cl = ' '.join(cll)
         assert cl > '', 'runCL needs a command line as clparms'
-        fd,templog = tempfile.mkstemp(suffix='rgtempRun.txt')
-        tlf = open(templog,'w')
+        fd, templog = tempfile.mkstemp(suffix='rgtempRun.txt')
+        tlf = open(templog, 'w')
         process = subprocess.Popen(cl, shell=True, stderr=tlf, stdout=tlf)
         rval = process.wait()
         tlf.close()
-        tlogs = ''.join(open(templog,'r').readlines())
+        tlogs = ''.join(open(templog, 'r').readlines())
         if len(tlogs) > 1:
-            s = '## executing %s returned status %d and log (stdout/stderr) records: \n%s\n' % (cl,rval,tlogs)
+            s = '## executing %s returned status %d and log (stdout/stderr) records: \n%s\n' % (cl, rval, tlogs)
         else:
-            s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl,rval)
-        os.unlink(templog) # always
-        if rval <> 0:
-            print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % (cl,rval)
-            print >> sys.stderr, '## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO
-            print >> sys.stderr, '## Please ensure %s is correctly installed and working on the command line -see http://code.google.com/p/weblogo' % WEBLOGO
+            s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl, rval)
+        os.unlink(templog)  # always
+        if rval != 0:
+            print('## rgWebLogo3.py error - executing %s returned error code %d' % (cl, rval), file=sys.stderr)
+            print('## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO, file=sys.stderr)
+            print('## Please ensure %s is correctly installed and working on the command line -see https://github.com/weblogo/weblogo' % WEBLOGO, file=sys.stderr)
             sys.exit(1)
         return s
 
-        
     def iter_fasta(self):
         """
         generator for fasta sequences from a file
         """
         aseq = []
         seqname = None
-        for i,row in enumerate(self.fastaf):
+        for i, row in enumerate(self.fastaf):
             if row.startswith(self.FASTASTARTSYM):
-                if seqname <> None: # already in a sequence
+                if seqname is not None:  # already in a sequence
                     s = ''.join(aseq)
-                    l = len(s)
-                    yield (seqname,l)
+                    ls = len(s)
+                    yield (seqname, ls)
                     seqname = row[1:].strip()
                     aseq = []
                 else:
                     if i > 0:
-                        print >> sys.stderr,'Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input,self.FASTASTARTSYM)
+                        print('Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input, self.FASTASTARTSYM), file=sys.stderr)
                         sys.exit(1)
                     else:
-                        seqname = row[1:].strip() 
-            else: # sequence row
-                if seqname == None:
-                    print >> sys.stderr,'Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input,self.FASTASTARTSYM)
-                    sys.exit(1) 
+                        seqname = row[1:].strip()
+            else:  # sequence row
+                if seqname is None:
+                    print('Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input, self.FASTASTARTSYM), file=sys.stderr)
+                    sys.exit(1)
                 else:
                     aseq.append(row.strip())
-                
-        if seqname <> None: # last one
-            l = len(''.join(aseq))
-            yield (seqname,l)
-                
-        
+
+        if seqname is not None:  # last one
+            las = len(''.join(aseq))
+            yield (seqname, las)
+
     def fcheck(self):
         """ are all fasta sequence same length?
         might be mongo big
@@ -97,61 +100,50 @@
         flen = None
         lasti = None
         f = self.iter_fasta()
-        for i,(seqname,seqlen) in enumerate(f):
+        for i, (seqname, seqlen) in enumerate(f):
             lasti = i
             if i == 0:
                 flen = seqlen
             else:
-                if seqlen <> flen:
-                    print >> sys.stderr,self.badseq % self.opts.input
+                if seqlen != flen:
+                    print(self.badseq % self.opts.input, file=sys.stderr)
                     sys.exit(1)
-        return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input, lasti+1, flen)
-
+        return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input, lasti + 1, flen)
 
     def run(self):
         check = self.fcheck()
         self.clparams['-f'] = self.opts.input
         self.clparams['-o'] = self.opts.output
-        self.clparams['-t'] = '"%s"' % self.opts.logoname # must be wrapped as a string       
-        self.clparams['-F'] = self.opts.outformat       
-        if self.opts.size <> None:
+        self.clparams['-t'] = '"%s"' % self.opts.logoname  # must be wrapped as a string
+        self.clparams['-F'] = self.opts.outformat
+        if self.opts.size is not None:
             self.clparams['-s'] = self.opts.size
-        if self.opts.lower <> None:
+        if self.opts.lower is not None:
             self.clparams['-l'] = self.opts.lower
-        if self.opts.upper <> None:
-            self.clparams['-u'] = self.opts.upper        
-        if self.opts.colours <> None:
+        if self.opts.upper is not None:
+            self.clparams['-u'] = self.opts.upper
+        if self.opts.colours is not None:
             self.clparams['-c'] = self.opts.colours
-        if self.opts.units <> None:
+        if self.opts.units is not None:
             self.clparams['-U'] = self.opts.units
         s = self.runCL()
-        return check,s
+        return check, s
 
 
 if __name__ == '__main__':
-    '''
-    called as
-<command interpreter="python"> 
-    rgWebLogo3.py --outformat $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours"
-#if $range.mode == 'part'
--l "$range.seqstart" -u "$range.seqend"
-#end if
-    </command>
-
-    '''
     op = optparse.OptionParser()
     op.add_option('-i', '--input', default=None)
     op.add_option('-F', '--outformat', default='png')
-    op.add_option('-s', '--size', default=None) 
+    op.add_option('-s', '--size', default=None)
     op.add_option('-o', '--output', default='rgWebLogo3')
     op.add_option('-t', '--logoname', default='rgWebLogo3')
     op.add_option('-c', '--colours', default=None)
     op.add_option('-l', '--lower', default=None)
-    op.add_option('-u', '--upper', default=None)  
-    op.add_option('-U', '--units', default=None)  
+    op.add_option('-u', '--upper', default=None)
+    op.add_option('-U', '--units', default=None)
     opts, args = op.parse_args()
-    assert opts.input <> None,'weblogo3 needs a -i parameter with a fasta input file - cannot open'
-    assert os.path.isfile(opts.input),'weblogo3 needs a valid fasta input file - cannot open %s' % opts.input
+    assert opts.input is not None, 'weblogo3 needs a -i parameter with a fasta input file - cannot open'
+    assert os.path.isfile(opts.input), 'weblogo3 needs a valid fasta input file - cannot open %s' % opts.input
     w = WL3(opts)
-    checks,s = w.run()
-    print >> sys.stdout, checks # for info
+    checks, s = w.run()
+    print(checks, file=sys.stdout)  # for info