Description: Use 2to3 to port to Python3
Bug-Debian: https://bugs.debian.org/938415
Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 12 Sep 2019 11:26:11 +0200

--- a/pRSEM/Gene.py
+++ b/pRSEM/Gene.py
@@ -124,7 +124,7 @@ def constructGenesFromTranscripts(transc
   genes = []
   gene_dict_id = {}
   for tr in transcripts:
-    if gene_dict_id.has_key(tr.gene_id):
+    if tr.gene_id in gene_dict_id:
       gene_dict_id[tr.gene_id].transcripts.append(tr)
       tr.gene = gene_dict_id[tr.gene_id]
     else:
@@ -137,7 +137,7 @@ def constructGenesFromTranscripts(transc
       gene_dict_id[tr.gene_id] = gene
       tr.gene = gene
 
-  map(lambda gene: gene.getStartEndTSSTESFromTranscripts(), genes);
+  list(map(lambda gene: gene.getStartEndTSSTESFromTranscripts(), genes));
 
   return genes;
 
--- a/pRSEM/Param.py
+++ b/pRSEM/Param.py
@@ -98,7 +98,7 @@ class Param:
 
 
   def __str__(self):
-    ss = [ "%-33s %s\n" % (key, val) for (key, val) in self.argdict.items()] + \
+    ss = [ "%-33s %s\n" % (key, val) for (key, val) in list(self.argdict.items())] + \
          [ "%-33s %s\n" % ('RSEM_temp_dir', self.temp_dir ) ] + \
          [ "%-33s %s\n" % ('pRSEM_scr_dir', self.prsem_scr_dir) ]
     return ''.join(ss)
@@ -109,7 +109,7 @@ class Param:
     import os
     prm = cls()
     prm.argdict = argdict
-    for (key, val) in argdict.items():
+    for (key, val) in list(argdict.items()):
       setattr(prm, key, val)
 
     if prm.imd_name is not None:
--- a/pRSEM/Prsem.py
+++ b/pRSEM/Prsem.py
@@ -1,4 +1,4 @@
-#!/bin/env python
+#!/usr/bin/python3
 
 __doc__="""
 
@@ -65,9 +65,9 @@ def buildTrainingSet(prm):
   The order is required by rsem-run-gibbs so that prior can be assigned to
   transcript correctly
   """
-  ogot_genes = filter(lambda g: len(g.transcripts) == 1 and
+  ogot_genes = [g for g in prm.genes if len(g.transcripts) == 1 and
                                 (g.end - g.start + 1) >=
-                                prm.TRAINING_GENE_MIN_LEN, prm.genes)
+                                prm.TRAINING_GENE_MIN_LEN]
 
   trs = [tr for g in ogot_genes for tr in g.transcripts]
 
@@ -127,7 +127,7 @@ def genPriorByCombinedTSSSignals(prm):
   """
   f_fout = open(prm.finfo_multi_targets, 'w')
   f_fout.write("targetid\tfaln\tfftrs\n")
-  for (tgtid, faln) in prm.targetid2fchipseq_alignment.items():
+  for (tgtid, faln) in list(prm.targetid2fchipseq_alignment.items()):
     fftrs = prm.imd_name + '_prsem.' + tgtid + '.all_tr_features'
     f_fout.write("%s\t%s\t%s\n" % (tgtid, faln, fftrs))
   f_fout.close()
--- a/pRSEM/Transcript.py
+++ b/pRSEM/Transcript.py
@@ -41,7 +41,7 @@ class Transcript:
     for (start, end) in self.exon_ranges:
       s += " %d %d" % (start, end);
     s += "\n";
-    for key in self.gtf_attr.keys():
+    for key in list(self.gtf_attr.keys()):
       for val in self.gtf_attr[key]:
         s += '%s "%s"; ' % (key, val);
     s = s.rstrip();
@@ -58,7 +58,7 @@ class Transcript:
     for feature_word in feature_words:
       feature_word.lstrip();
       (key, val) = feature_word.split();
-      if not self.gtf_attr.has_key(key):
+      if key not in self.gtf_attr:
         self.gtf_attr[key] = [];
       self.gtf_attr[key].append(val.strip('"'));
 
@@ -160,7 +160,7 @@ def readRSEMTI(fin):
     tr.constructFromRSEMTI(lines[i*6+1:i*6+7]);
     transcripts.append(tr);
     if (i > 0) and (i % 20000 == 0):
-      print "processed %d transcripts" % i;
+      print("processed %d transcripts" % i);
 
   return transcripts;
 
@@ -183,7 +183,7 @@ def quicklyReadRSEMTI(fin):
     tr.quicklyConstructFromRSEMTI(lines[i*6+1:i*6+7]);
     transcripts.append(tr);
     if (i > 0) and (i % 20000 == 0):
-      print "processed %d transcripts" % i;
+      print("processed %d transcripts" % i);
 
   return transcripts;
 
--- a/pRSEM/Util.py
+++ b/pRSEM/Util.py
@@ -60,7 +60,7 @@ def runCommandAndGetOutput(*args, **kwar
 
   try:
     output = subprocess.check_output(str_args)
-  except subprocess.CalledProcessError, e:
+  except subprocess.CalledProcessError as e:
     sys.exit("\nExecution failed: %s\n" % e.output)
 
   return output
@@ -123,14 +123,14 @@ def runMPOverAList(nprocs, func, args):
   if len(args[0]) > nprocs:
     chunksize = len(args[0])/nprocs + 1
   procs = []
-  for i in xrange(nprocs):
+  for i in range(nprocs):
     list_args = [args[0][chunksize*i:chunksize*(i+1)]] + args[1:] + [out_q]
     p = mp.Process(target = func, args = tuple(list_args))
     procs.append(p)
     p.start()
 
   dict_to_return = {}
-  for i in xrange(nprocs):
+  for i in range(nprocs):
     dict_to_return.update(out_q.get())
 
   for p in procs:
--- a/pRSEM/prsem-calculate-expression
+++ b/pRSEM/prsem-calculate-expression
@@ -1,4 +1,4 @@
-#!/bin/env python
+#!/usr/bin/python3
 
 __doc__="""
 
--- a/pRSEM/prsem-prepare-reference
+++ b/pRSEM/prsem-prepare-reference
@@ -1,4 +1,4 @@
-#!/bin/env python
+#!/usr/bin/python3
 
 __doc__="""
 
--- a/pRSEM/prsem-testing-procedure
+++ b/pRSEM/prsem-testing-procedure
@@ -1,4 +1,4 @@
-#!/bin/env python
+#!/usr/bin/python3
 
 __doc__="""
 
--- a/rsem-gff3-to-gtf
+++ b/rsem-gff3-to-gtf
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2016
 # Bo Li (University of California, Berkeley)
--- a/rsem-refseq-extract-primary-assembly
+++ b/rsem-refseq-extract-primary-assembly
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 from sys import argv, exit