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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
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