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debian/control
View file @ e031130c
......@@ -4,9 +4,9 @@ Uploaders: Tobias Hamp <hampt@rostlab.org>,
Laszlo Kajan <lkajan@debian.org>
Section: science
Priority: optional
Build-Depends-Indep: debhelper (>= 11~),
Build-Depends-Indep: debhelper (>= 12~),
dh-python,
python,
python3-all,
javahelper,
default-jdk
Standards-Version: 4.2.1
......@@ -18,8 +18,8 @@ Package: metastudent
Architecture: all
Depends: ${misc:Depends},
${perl:Depends},
${python:Depends},
python,
${python3:Depends},
python3,
blast2,
default-jre,
libgo-perl (>= 0.15-3),
......
debian/patches/2to3.patch 0 → 100644
View file @ e031130c
Description: use 2to3 to port python2 files to python3
Author: Shayan Doust <hello@shayandoust.me>
Bug-Debian: https://bugs.debian.org/937017
Last-Update: 2019-09-16
---
Index: metastudent/metastudentPkg/Logger.py
===================================================================
--- metastudent.orig/metastudentPkg/Logger.py 2019-09-16 20:56:44.666912957 +0100
+++ metastudent/metastudentPkg/Logger.py 2019-09-16 20:56:44.662912926 +0100
@@ -23,9 +23,9 @@
@classmethod
def log(cls, msg, level=0):
if level==0:
- print msg
+ print(msg)
else:
- print >> sys.stderr,msg
+ print(msg, file=sys.stderr)
#cls.internalLogger.info(msg)
Index: metastudent/metastudentPkg/commons.py
===================================================================
--- metastudent.orig/metastudentPkg/commons.py 2019-09-16 20:56:44.666912957 +0100
+++ metastudent/metastudentPkg/commons.py 2019-09-16 20:56:44.662912926 +0100
@@ -10,6 +10,7 @@
import shlex
import time
from multiprocessing.pool import Pool
+from functools import reduce
mfRoot = "GO:0003674"
bpRoot = "GO:0008150"
@@ -30,12 +31,12 @@
def p(string):
if not silent:
- print string
+ print(string)
def getPkgPath():
myPath=""
if hasattr(sys, "frozen"):
- myPath = os.path.dirname(unicode(sys.executable, sys.getfilesystemencoding( )))
+ myPath = os.path.dirname(str(sys.executable, sys.getfilesystemencoding( )))
else:
myPath = os.path.dirname(os.path.abspath(__file__))
return myPath
@@ -116,7 +117,7 @@
fastaFile = open(fastaFilePath,'w')
fastaFile.write("\n".join(newLines))
fastaFile.close()
- except (IOError, os.error), why:
+ except (IOError, os.error) as why:
Logger.log("Error reading/writing fasta file " + str(why))
@@ -131,11 +132,11 @@
- termsToScoresLocal = dict([(key,val) for (key,val) in termsToScores.iteritems() if key in go.fullClosureKeys])
+ termsToScoresLocal = dict([(key,val) for (key,val) in termsToScores.items() if key in go.fullClosureKeys])
- allNodes = frozenset(go.getAllParents(termsToScoresLocal.keys()) | set(termsToScoresLocal.keys()) )
+ allNodes = frozenset(go.getAllParents(list(termsToScoresLocal.keys())) | set(termsToScoresLocal.keys()) )
@@ -157,11 +158,11 @@
- if bpRoot in termsToScoresLocal.keys():
+ if bpRoot in list(termsToScoresLocal.keys()):
del termsToScoresLocal[bpRoot]
- if mfRoot in termsToScoresLocal.keys():
+ if mfRoot in list(termsToScoresLocal.keys()):
del termsToScoresLocal[mfRoot]
- if ccRoot in termsToScoresLocal.keys():
+ if ccRoot in list(termsToScoresLocal.keys()):
del termsToScoresLocal[ccRoot]
return termsToScoresLocal
@@ -241,7 +242,7 @@
for root in allValues - set(self.fullClosure.keys()):
self.fullClosure[root] = set([])
- self.fullClosureKeys = frozenset(self.fullClosure.keys())
+ self.fullClosureKeys = frozenset(list(self.fullClosure.keys()))
def getAllParents(self, terms):
returnTerms = set([])
@@ -323,7 +324,7 @@
def toOutputLines(self):
lines = []
for targetId in self.targetsSorted:
- for term, scorei in sorted(self.targetToTermToScore[targetId].items(), key=lambda x: x[1], reverse=True):
+ for term, scorei in sorted(list(self.targetToTermToScore[targetId].items()), key=lambda x: x[1], reverse=True):
lines.append("%s\t%s\t%.2f\n" % (decodeFastaHeader(targetId), term, scorei) )
return lines
@@ -331,7 +332,7 @@
def toOutputLinesWithNames(self):
lines = []
for targetId in self.targetsSorted:
- for term, scorei in sorted(self.targetToTermToScore[targetId].items(), key=lambda x: x[1], reverse=True):
+ for term, scorei in sorted(list(self.targetToTermToScore[targetId].items()), key=lambda x: x[1], reverse=True):
lines.append("%s\t%s\t%.2f\t%s\n" % (decodeFastaHeader(targetId), term, scorei, self.go.termToName.get(term, "n/a") ))
return lines
Index: metastudent/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py
===================================================================
--- metastudent.orig/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py 2019-09-16 20:56:44.666912957 +0100
+++ metastudent/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py 2019-09-16 20:56:44.662912926 +0100
@@ -37,17 +37,17 @@
outfile.write(go+'\n'+sq+'\n')
sqCounter+=1
if (sqCounter%50000 == 0 and sqCounter!=0):
- print("%(sqCounter)d Sequences written into %(outfile)s" % {
+ print(("%(sqCounter)d Sequences written into %(outfile)s" % {
'sqCounter': sqCounter,
- 'outfile': outfileName})
+ 'outfile': outfileName}))
go = ''
sq = ''
break
else:
sq = sq + line.lstrip()
- print("%(sqCounter)d Sequences written into %(outfile)s\nfinished" % {
+ print(("%(sqCounter)d Sequences written into %(outfile)s\nfinished" % {
'sqCounter': sqCounter,
- 'outfile': outfileName})
+ 'outfile': outfileName}))
# close outfile
outfile.close()
Index: metastudent/metastudentPkg/lib/groupA/parser/group2_goStatistics.py
===================================================================
--- metastudent.orig/metastudentPkg/lib/groupA/parser/group2_goStatistics.py 2019-09-16 20:56:44.666912957 +0100
+++ metastudent/metastudentPkg/lib/groupA/parser/group2_goStatistics.py 2019-09-16 20:56:44.662912926 +0100
@@ -36,11 +36,11 @@
goPerSeqDiamFloored = int(math.floor(goPerSeqDiam))
# output of the statistics
- print("%s protein sequences with GO term found" % seqCount)
- print("%s protein sequences with just one GO found" % seqWithOneGo)
- print("%(goPSDF)s GOs per sequence averagely found (%(goPSD)s)" % {
+ print(("%s protein sequences with GO term found" % seqCount))
+ print(("%s protein sequences with just one GO found" % seqWithOneGo))
+ print(("%(goPSDF)s GOs per sequence averagely found (%(goPSD)s)" % {
'goPSDF': goPerSeqDiamFloored,
- 'goPSD': goPerSeqDiam})
+ 'goPSD': goPerSeqDiam}))
Index: metastudent/metastudentPkg/runMethods.py
===================================================================
--- metastudent.orig/metastudentPkg/runMethods.py 2019-09-16 20:56:44.666912957 +0100
+++ metastudent/metastudentPkg/runMethods.py 2019-09-16 20:56:44.662912926 +0100
@@ -5,9 +5,9 @@
'''
import os
-import commands
-from Logger import Logger
-from BlastWrapper import blastallParameters, createBlastPGPCommand
+import subprocess
+from .Logger import Logger
+from .BlastWrapper import blastallParameters, createBlastPGPCommand
from metastudentPkg.commons import p, splitBigFastaFile
import sys
import shlex
@@ -37,7 +37,7 @@
#
# executeCommandInSGELocalAsyncJoin()
- s, o = commands.getstatusoutput(blastCommand)
+ s, o = subprocess.getstatusoutput(blastCommand)
if s != 0:
Logger.log("!!!Error!!! " + blastCommand)
Logger.log(s)
@@ -77,15 +77,15 @@
else:
logFile = open(logPath, 'a')
- s, o = commands.getstatusoutput(commandString)
+ s, o = subprocess.getstatusoutput(commandString)
if True:#s != 0:
logFile.write("Command: " + commandString + "\n")
logFile.write(str(s)+"\n")
logFile.write(o+"\n")
if s != 0:
- print >> sys.stderr,"!!!Error!!! " + commandString
- print >> sys.stderr,str(s)
- print >> sys.stderr,o
+ print("!!!Error!!! " + commandString, file=sys.stderr)
+ print(str(s), file=sys.stderr)
+ print(o, file=sys.stderr)
#raise
logFile.close()
@@ -136,15 +136,15 @@
else:
logFile = open(logPath, 'a')
- s, o = commands.getstatusoutput(commandString)
+ s, o = subprocess.getstatusoutput(commandString)
if True:#s != 0:
logFile.write("Command: " + commandString + "\n")
logFile.write(str(s) + "\n")
logFile.write(o+ "\n")
if s != 0:
- print >> sys.stderr,"!!!Error!!! " + commandString
- print >> sys.stderr,str(s)
- print >> sys.stderr,o
+ print("!!!Error!!! " + commandString, file=sys.stderr)
+ print(str(s), file=sys.stderr)
+ print(o, file=sys.stderr)
#raise
logFile.close()
@@ -180,7 +180,7 @@
"./CafaWrapper3.pl %s %s %s %s" % (blastOutputFilePath, outputFilePath, scoring, tmpDirPath)]
commandString = ";".join(commandsi)
if debug:
- print >> sys.stderr, commandString
+ print(commandString, file=sys.stderr)
os.chdir(currCwd)
logFile=None
@@ -190,15 +190,15 @@
else:
logFile = open(logPath, 'a')
- s, o = commands.getstatusoutput(commandString)
+ s, o = subprocess.getstatusoutput(commandString)
if True:#s != 0:
logFile.write("Command: " + commandString)
logFile.write(str(s))
logFile.write(o)
if s != 0:
- print >> sys.stderr, "!!!Error!!! " + commandString
- print >> sys.stderr,str(s)
- print >> sys.stderr,o
+ print("!!!Error!!! " + commandString, file=sys.stderr)
+ print(str(s), file=sys.stderr)
+ print(o, file=sys.stderr)
#raise
logFile.close()
Index: metastudent/setup.py
===================================================================
--- metastudent.orig/setup.py 2019-09-16 20:56:44.666912957 +0100
+++ metastudent/setup.py 2019-09-16 20:56:44.662912926 +0100
@@ -11,13 +11,13 @@
import tempfile
-print 'Creating man page metastudent.1...'
+print('Creating man page metastudent.1...')
childP = Popen(["pod2man", "-c", "'User Commands'", "-r", "'%s'", "-name", "METASTUDENT", "metastudent", "metastudent.1"], stdout=PIPE, stderr=PIPE)
stdout, stderr = childP.communicate()
if childP.poll() != 0:
- print >> sys.stderr, "Error: pod2man failed"
- print >> sys.stderr, "Stdout: %s" % (stdout)
- print >> sys.stderr, "Stderr: %s" % (stderr)
+ print("Error: pod2man failed", file=sys.stderr)
+ print("Stdout: %s" % (stdout), file=sys.stderr)
+ print("Stderr: %s" % (stderr), file=sys.stderr)
sys.exit(1)
@@ -38,32 +38,32 @@
for path, dirs, files in os.walk(os.path.join(pkgPath, "lib")):
if "/.svn" not in path:
for dir in dirs:
- os.chmod(os.path.join(path, dir),0755)
+ os.chmod(os.path.join(path, dir),0o755)
for filename in files:
if not filename.endswith(".java"):
filenameSplit = filename.split(".")
if len(filenameSplit) > 2 and "."+filenameSplit[-1] in exeSuffixes:
- os.chmod(os.path.join(path, filename),0755)
+ os.chmod(os.path.join(path, filename),0o755)
else:
- os.chmod(os.path.join(path, filename),0644)
+ os.chmod(os.path.join(path, filename),0o644)
dataFiles.append(os.path.relpath(os.path.join(path, filename), pkgPath))
if filename in executables:
- os.chmod(os.path.join(path, filename),0755)
+ os.chmod(os.path.join(path, filename),0o755)
metastudentPath=""
if hasattr(sys, "frozen"):
- metastudentPath=os.path.dirname(unicode(sys.executable, sys.getfilesystemencoding( )))
+ metastudentPath=os.path.dirname(str(sys.executable, sys.getfilesystemencoding( )))
else:
metastudentPath = os.path.dirname(os.path.abspath(__file__))
for filei in os.listdir(metastudentPath):
fileAbs = os.path.join(metastudentPath, filei)
if os.path.isdir(fileAbs):
- os.chmod(os.path.join(metastudentPath, filei),0755)
+ os.chmod(os.path.join(metastudentPath, filei),0o755)
else:
- os.chmod(os.path.join(metastudentPath, filei),0644)
+ os.chmod(os.path.join(metastudentPath, filei),0o644)
-os.chmod(os.path.join(metastudentPath, "metastudent"),0755);
-os.chmod(os.path.join(metastudentPath, "setup.py"),0755);
+os.chmod(os.path.join(metastudentPath, "metastudent"),0o755);
+os.chmod(os.path.join(metastudentPath, "setup.py"),0o755);
#metastudentPath=""
#if hasattr(sys, "frozen"):
debian/patches/series
View file @ e031130c
2to3.patch
01_fix_blastp.patch
debian/rules
View file @ e031130c
......@@ -8,7 +8,7 @@ JAVA_HOME=/usr/lib/jvm/default-java
include /usr/share/dpkg/default.mk
%:
dh $@ --with javahelper --with python2
dh $@ --with javahelper --with python3 --buildsystem=pybuild
override_dh_auto_clean:
dh_auto_clean
......