[med-svn] [Git][med-team/kmer][master] 4 commits: Make sure simple names for dynamic libraries are made available
Andreas Tille
gitlab at salsa.debian.org
Thu Dec 19 19:30:42 GMT 2019
Andreas Tille pushed to branch master at Debian Med / kmer
Commits:
57c585a2 by Andreas Tille at 2019-12-19T12:50:51Z
Make sure simple names for dynamic libraries are made available
- - - - -
d10f0318 by Andreas Tille at 2019-12-19T14:37:05Z
Some more fixes.
- - - - -
9d3a3aa8 by Andreas Tille at 2019-12-19T16:12:24Z
Finally found some remaining Python2 call inside Perl script
- - - - -
ce992860 by Andreas Tille at 2019-12-19T19:30:21Z
There is no file class in Python3
- - - - -
3 changed files:
- debian/changelog
- debian/patches/2to3.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -14,6 +14,7 @@ kmer (0~20150903+r2013-7) UNRELEASED; urgency=medium
lines.
* Remove obsolete field Name from debian/upstream/metadata (already
present in machine-readable debian/copyright).
+ TODO: Tests are failing
-- Andreas Tille <tille at debian.org> Thu, 19 Dec 2019 10:43:09 +0100
=====================================
debian/patches/2to3.patch
=====================================
@@ -25,25 +25,31 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
"""
The environmental variable "PYTHONPATH" is a colon separated list
-@@ -32,7 +32,7 @@ STDERR=sys.stderr
- STDOUT=sys.stdout
+@@ -28,12 +28,9 @@ import fillIntraRunGaps
+ #import dedashMatches
+
+-STDERR=sys.stderr
+-STDOUT=sys.stdout
+-
def die(message):
- print >>STDERR, message
-+ print(message, file=STDERR)
- os.exit(1)
+- os.exit(1)
++ print(message, file=sys.stderr)
++ sys.exit(1)
def cvm(f,x,y):
-@@ -58,7 +58,7 @@ class GlobalParam:
+ # A cvm variant (flag ? y : x) = (x,y)[f]
+@@ -58,7 +55,7 @@ class GlobalParam:
def usage (*_):
- print >>STDERR, "Usage: atacdriver.py matchFilePrefix"
-+ print("Usage: atacdriver.py matchFilePrefix", file=STDERR)
++ print("Usage: atacdriver.py matchFilePrefix", file=sys.stderr)
# end def
def filterByMatchLength( inpfile, outfile, minimum_length):
-@@ -69,7 +69,7 @@ def filterByMatchLength( inpfile, outfil
+@@ -69,7 +66,7 @@ def filterByMatchLength( inpfile, outfil
FM = MatchRecord.MatchRecord(line)
if (FM.x_length >= minimum_length and
FM.y_length >= minimum_length ):
@@ -52,7 +58,7 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
# end if
# end if
# end for
-@@ -90,7 +90,7 @@ def onlyKeepLongRuns ( inpfile, outname,
+@@ -90,7 +87,7 @@ def onlyKeepLongRuns ( inpfile, outname,
SL = FM.x_length
if FL != None and FL.runid != FM.runid :
for x in store:
@@ -61,7 +67,7 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
# end for
store = []
lenInMatches = SL
-@@ -102,10 +102,10 @@ def onlyKeepLongRuns ( inpfile, outname,
+@@ -102,10 +99,10 @@ def onlyKeepLongRuns ( inpfile, outname,
store.append(FM)
else:
for x in store:
@@ -74,7 +80,7 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
# end if
FL = FM
# end if
-@@ -142,10 +142,10 @@ def coalesceMatches ( inpfile, outfile,
+@@ -142,10 +139,10 @@ def coalesceMatches ( inpfile, outfile,
assert(py >= 0)
assert(ny >= 0)
if (not (not needs_to_share_diagonal or nx == ny)):
@@ -82,14 +88,14 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
- print >>STDERR, str(curF)
- print >>STDERR, 'needs_to_share_diagonal=' + str(needs_to_share_diagonal)
- print >>STDERR, 'nx=' + str(nx) + ' ny=' + str(ny)
-+ print('Bombed on:', file=STDERR)
-+ print(str(curF), file=STDERR)
-+ print('needs_to_share_diagonal=' + str(needs_to_share_diagonal), file=STDERR)
-+ print('nx=' + str(nx) + ' ny=' + str(ny), file=STDERR)
++ print('Bombed on:', file=sys.stderr)
++ print(str(curF), file=sys.stderr)
++ print('needs_to_share_diagonal=' + str(needs_to_share_diagonal), file=sys.stderr)
++ print('nx=' + str(nx) + ' ny=' + str(ny), file=sys.stderr)
# end if
assert((hghHitPX == None or (not needs_to_share_diagonal) or nx == ny))
forward = (curF.x_orientation == curF.y_orientation)
-@@ -182,7 +182,7 @@ def coalesceMatches ( inpfile, outfile,
+@@ -182,7 +179,7 @@ def coalesceMatches ( inpfile, outfile,
firstF.y_start = lowHitPY
firstF.x_length = hghHitPX - lowHitPX
firstF.y_length = hghHitPY - lowHitPY
@@ -98,7 +104,7 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
# end if
firstF = curF
lowHitPX = lowMerPX
-@@ -209,7 +209,7 @@ def coalesceMatches ( inpfile, outfile,
+@@ -209,7 +206,7 @@ def coalesceMatches ( inpfile, outfile,
firstF.y_start = lowHitPY
firstF.x_length = hghHitPX - lowHitPX
firstF.y_length = hghHitPY - lowHitPY
@@ -107,7 +113,7 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
return
# end def
-@@ -243,12 +243,12 @@ def boxRecovery( inpfile, rawfile, outna
+@@ -243,12 +240,12 @@ def boxRecovery( inpfile, rawfile, outna
if( rawline[0] == 'M'):
rawMatch = MatchRecord.MatchRecord(rawline)
if(rawMatch.sameAs(rightMatch)):
@@ -122,7 +128,7 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
# end if
# end if
# end if
-@@ -260,7 +260,7 @@ def boxRecovery( inpfile, rawfile, outna
+@@ -260,7 +257,7 @@ def boxRecovery( inpfile, rawfile, outna
if( rawline[0] == 'M'):
rawMatch = MatchRecord.MatchRecord(rawline)
if(rawMatch.sameAs(rightMatch)):
@@ -131,16 +137,16 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
break
else:
# print >>STDERR, "Discard rawMatch=", rawMatch
-@@ -281,7 +281,7 @@ def boxRecovery( inpfile, rawfile, outna
+@@ -281,7 +278,7 @@ def boxRecovery( inpfile, rawfile, outna
class AtacDriver(AtacFile.AtacFile):
def runOld(self):
self.globals['atacAlgorithmVersion'] = str(17)
- print >>STDERR, "runName = %s\n" % self.runName
-+ print("runName = %s\n" % self.runName, file=STDERR)
++ print("runName = %s\n" % self.runName, file=sys.stderr)
# The ATAC globals used by this script:
opt_t = int(self.globals['globalMatchMinSize'])
-@@ -295,7 +295,7 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -295,7 +292,7 @@ class AtacDriver(AtacFile.AtacFile):
assemblyFile2 = self.globals['assemblyFile2']
boxRecoveryOn = 0 # Deprecated for same species comparisons 2003/09/09.
@@ -149,7 +155,7 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
boxRecoveryOn = int(self.globals['boxRecoveryOn'])
t0 = time.time()
-@@ -309,24 +309,24 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -309,24 +306,24 @@ class AtacDriver(AtacFile.AtacFile):
redo = 0
keep = 0
step = 0
@@ -162,9 +168,9 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
- print >>STDERR, 'Keep step=' + str(keep)
- print >>STDERR, 'At step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
-+ print('Keep step=' + str(keep), file=STDERR)
-+ print('At step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('Keep step=' + str(keep), file=sys.stderr)
++ print('At step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
outprefix = self.runName
@@ -172,83 +178,83 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
- print >>STDERR, 'At uniqueFilter, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At uniqueFilter, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At uniqueFilter, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- if(not(self.globals.has_key('uniqueFilterOn') and self.globals['uniqueFilterOn']=="0")):
- print >>STDERR, 'Running UniqueFilter'
+ if(not('uniqueFilterOn' in self.globals and self.globals['uniqueFilterOn']=="0")):
-+ print('Running UniqueFilter', file=STDERR)
++ print('Running UniqueFilter', file=sys.stderr)
outfile = MyFile.myfile()
UniqueFilter.main( self.matches, outfile)
self.matches = outfile
-@@ -334,11 +334,11 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -334,11 +331,11 @@ class AtacDriver(AtacFile.AtacFile):
self.checkpoint(outprefix)
step += 1
- print >>STDERR, 'At filterByMatchLength, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At filterByMatchLength, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At filterByMatchLength, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, 'Running filterByMatchLength'
-+ print('Running filterByMatchLength', file=STDERR)
++ print('Running filterByMatchLength', file=sys.stderr)
outfile = MyFile.myfile()
filterByMatchLength( self.matches, outfile, opt_t)
self.matches = outfile
-@@ -346,15 +346,15 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -346,15 +343,15 @@ class AtacDriver(AtacFile.AtacFile):
self.checkpoint(outprefix)
step += 1
- print >>STDERR, 'At trimMatchOverlaps, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At trimMatchOverlaps, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At trimMatchOverlaps, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, "Start trimming for bp one-to-one-ness"
-+ print("Start trimming for bp one-to-one-ness", file=STDERR)
++ print("Start trimming for bp one-to-one-ness", file=sys.stderr)
tempdata = MyFile.myfile()
TrimMatchOverlaps.trimMatchOverlapsInBoth(self.matches,tempdata,'u')
self.matches = tempdata
- print >>STDERR, "Finished trimming for bp one-to-one-ness"
-+ print("Finished trimming for bp one-to-one-ness", file=STDERR)
++ print("Finished trimming for bp one-to-one-ness", file=sys.stderr)
outprefix += '.trim'
self.checkpoint(outprefix)
-@@ -363,11 +363,11 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -363,11 +360,11 @@ class AtacDriver(AtacFile.AtacFile):
rawfile = self.matches
step += 1
- print >>STDERR, 'At formPerfectRuns, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At formPerfectRuns, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At formPerfectRuns, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, 'from ' + outprefix + ' making ' + outprefix + '.p6'
-+ print('from ' + outprefix + ' making ' + outprefix + '.p6', file=STDERR)
++ print('from ' + outprefix + ' making ' + outprefix + '.p6', file=sys.stderr)
tempdata = PerfectRuns.formPerfectRuns(self.matches,
MatchRecord.sortInXorderAP,
MatchRecord.sortInYorderAP,
-@@ -378,22 +378,22 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -378,22 +375,22 @@ class AtacDriver(AtacFile.AtacFile):
# end if
step += 1
- print >>STDERR, 'At onlyKeepLongRuns, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At onlyKeepLongRuns, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At onlyKeepLongRuns, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, 'from ' + outprefix + ' making ' + outprefix + '.l' + str(opt_l)
-+ print('from ' + outprefix + ' making ' + outprefix + '.l' + str(opt_l), file=STDERR)
++ print('from ' + outprefix + ' making ' + outprefix + '.l' + str(opt_l), file=sys.stderr)
tempdata = onlyKeepLongRuns( self.matches, outprefix, opt_l)
self.matches = tempdata
outprefix += '.l' + str(opt_l)
@@ -258,39 +264,39 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
- print >>STDERR, 'At formPerfectRuns, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At formPerfectRuns, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At formPerfectRuns, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, 'Heal the perfect runs'
-+ print('Heal the perfect runs', file=STDERR)
++ print('Heal the perfect runs', file=sys.stderr)
tempdata = PerfectRuns.formPerfectRuns(self.matches,
MatchRecord.sortInYorderAP,
MatchRecord.sortInXorderAP, maxdiff, 'r')
-@@ -405,16 +405,16 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -405,16 +402,16 @@ class AtacDriver(AtacFile.AtacFile):
# This is a box recovery step.
step += 1
- print >>STDERR, 'At boxRecovery, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At boxRecovery, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At boxRecovery, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, 'from ' + outprefix + ' making ' + outprefix + '.br'
- print >>STDERR, "Make sorted raw matches"
-+ print('from ' + outprefix + ' making ' + outprefix + '.br', file=STDERR)
-+ print("Make sorted raw matches", file=STDERR)
++ print('from ' + outprefix + ' making ' + outprefix + '.br', file=sys.stderr)
++ print("Make sorted raw matches", file=sys.stderr)
outfile = MyFile.myfile()
MatchRecord.sortInXorderAP( rawfile, outfile)
rawfile = outfile
- print >>STDERR, "perform box recovery"
-+ print("perform box recovery", file=STDERR)
++ print("perform box recovery", file=sys.stderr)
tempdata = boxRecovery( self.matches, rawfile, outprefix)
self.matches = tempdata
outprefix += '.br'
-@@ -422,12 +422,12 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -422,12 +419,12 @@ class AtacDriver(AtacFile.AtacFile):
# end if
step += 1
@@ -298,58 +304,58 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ( (keep < step) and not self.globals.has_key(ckpName))):
- print >>STDERR, "form perfect runs"
-+ print('At formPerfectRuns, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At formPerfectRuns, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ( (keep < step) and ckpName not in self.globals)):
-+ print("form perfect runs", file=STDERR)
++ print("form perfect runs", file=sys.stderr)
redo = 1
- print >>STDERR, 'from ' + outprefix + ' to ' + outprefix + '.p6'
-+ print('from ' + outprefix + ' to ' + outprefix + '.p6', file=STDERR)
++ print('from ' + outprefix + ' to ' + outprefix + '.p6', file=sys.stderr)
tempdata = PerfectRuns.formPerfectRuns(self.matches,
MatchRecord.sortInXorderAP,
MatchRecord.sortInYorderAP, maxdiff, 'r')
-@@ -436,11 +436,11 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -436,11 +433,11 @@ class AtacDriver(AtacFile.AtacFile):
self.checkpoint(outprefix)
step += 1
- print >>STDERR, 'At squeezeIntraRunGaps, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At squeezeIntraRunGaps, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At squeezeIntraRunGaps, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, 'from ' + outprefix + ' to ' + outprefix + '.sq'
-+ print('from ' + outprefix + ' to ' + outprefix + '.sq', file=STDERR)
++ print('from ' + outprefix + ' to ' + outprefix + '.sq', file=sys.stderr)
tempdata = MyFile.myfile()
squeezeIntraRunGaps.mainLoop(
self.matches,
-@@ -454,39 +454,39 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -454,39 +451,39 @@ class AtacDriver(AtacFile.AtacFile):
self.checkpoint(outprefix)
step += 1
- print >>STDERR, 'At TrimMatchOverlaps, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At TrimMatchOverlaps, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At TrimMatchOverlaps, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, "Start trimming for bp one-to-one-ness"
-+ print("Start trimming for bp one-to-one-ness", file=STDERR)
++ print("Start trimming for bp one-to-one-ness", file=sys.stderr)
tempdata = MyFile.myfile()
TrimMatchOverlaps.trimMatchOverlapsInBoth(self.matches,tempdata,'u')
self.matches = tempdata
outprefix += '.trim'
- print >>STDERR, "Finished trimming for bp one-to-one-ness"
-+ print("Finished trimming for bp one-to-one-ness", file=STDERR)
++ print("Finished trimming for bp one-to-one-ness", file=sys.stderr)
step += 1
- print >>STDERR, 'At RunsAsMatches, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At RunsAsMatches, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At RunsAsMatches, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
self.runs = PerfectRuns.runsAsMatches( self.matches)
@@ -365,13 +371,13 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
- print >>STDERR, 'At fillIntraRunGaps, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At fillIntraRunGaps, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At fillIntraRunGaps, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, "fill the intrarun gaps"
- if(not self.globals.has_key('fillIntraRunGapsErate')):
-+ print("fill the intrarun gaps", file=STDERR)
++ print("fill the intrarun gaps", file=sys.stderr)
+ if('fillIntraRunGapsErate' not in self.globals):
self.globals['fillIntraRunGapsErate'] = 0.10
- if(not self.globals.has_key('fillIntraRunGapsMaxGap')):
@@ -379,37 +385,37 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
self.globals['fillIntraRunGapsMaxGap'] = 100000
fillIntraRunGapsErate = float(self.globals['fillIntraRunGapsErate'])
fillIntraRunGapsMaxGap = int(self.globals['fillIntraRunGapsMaxGap'])
-@@ -499,11 +499,11 @@ class AtacDriver(AtacFile.AtacFile):
+@@ -499,11 +496,11 @@ class AtacDriver(AtacFile.AtacFile):
self.checkpoint(outprefix)
step += 1
- print >>STDERR, 'At TrimMatchOverlaps, step=' + str(step)
- print >>STDERR, 'Time elapsed=' + str(time.time()-t0)
- if (redo or ((keep < step) and not self.globals.has_key(ckpName))):
-+ print('At TrimMatchOverlaps, step=' + str(step), file=STDERR)
-+ print('Time elapsed=' + str(time.time()-t0), file=STDERR)
++ print('At TrimMatchOverlaps, step=' + str(step), file=sys.stderr)
++ print('Time elapsed=' + str(time.time()-t0), file=sys.stderr)
+ if (redo or ((keep < step) and ckpName not in self.globals)):
redo = 1
- print >>STDERR, "trim the overlaps"
-+ print("trim the overlaps", file=STDERR)
++ print("trim the overlaps", file=sys.stderr)
tempdata = MyFile.myfile()
TrimMatchOverlaps.trimMatchOverlapsInBoth(self.matches,tempdata,'u')
self.matches = tempdata
-@@ -522,7 +522,7 @@ class localExecutable :
+@@ -522,7 +519,7 @@ class localExecutable :
self.name = name
def run(self,argline,inpfile,outfile):
cmd = "%s %s %s %s" % (self.name,argline,inpfile,outfile)
- print >>STDERR,"cmd =", cmd
-+ print("cmd =", cmd, file=STDERR)
++ print("cmd =", cmd, file=sys.stderr)
iret = os.system(cmd)
assert(iret == 0)
-@@ -533,14 +533,14 @@ def main(runName):
+@@ -533,14 +530,14 @@ def main(runName):
obj = AtacDriver(runName)
t1 = time.time()
- print >>STDERR, "Read checkpoint in %d seconds." % (t1-t0)
-+ print("Read checkpoint in %d seconds." % (t1-t0), file=STDERR)
++ print("Read checkpoint in %d seconds." % (t1-t0), file=sys.stderr)
t0=t1
# The following are required:
@@ -424,14 +430,14 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
assemblyId1 = obj.globals['assemblyId1']
assemblyId2 = obj.globals['assemblyId2']
-@@ -560,33 +560,33 @@ def main(runName):
+@@ -560,33 +557,33 @@ def main(runName):
assert(os.path.exists(assemblyFile1+".idxStore"))
assert(os.path.exists(assemblyFile2+".idxStore"))
- if not obj.globals.has_key('matchesFile'):
- print >>STDERR, "We need to make the raw matches."
+ if 'matchesFile' not in obj.globals:
-+ print("We need to make the raw matches.", file=STDERR)
++ print("We need to make the raw matches.", file=sys.stderr)
- if(not obj.globals.has_key('rawMatchMerSize')):
+ if('rawMatchMerSize' not in obj.globals):
@@ -464,11 +470,11 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
t1 = time.time()
- print >>STDERR, "Ran in %d seconds." % (t1-t0)
-+ print("Ran in %d seconds." % (t1-t0), file=STDERR)
++ print("Ran in %d seconds." % (t1-t0), file=sys.stderr)
obj.checkpoint(runName + ".chained.atac")
-@@ -594,7 +594,7 @@ def main(runName):
+@@ -594,7 +591,7 @@ def main(runName):
if __name__ == '__main__':
if (len(sys.argv) == 1):
@@ -594,7 +600,7 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
# end def
--- a/atac-driver/chainer/python/MyFile.py
+++ b/atac-driver/chainer/python/MyFile.py
-@@ -1,5 +1,5 @@
+@@ -1,9 +1,9 @@
-#!/usr/bin/env python
-import sys, os, copy, tempfile, cStringIO
+#!/usr/bin/python3
@@ -602,6 +608,11 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
# from __future__ import generators # Necessary before Python 2.3
+-class myfile(file):
++class myfile():
+ "A temporary anonymous file"
+ def __init__(self):
+ filename = tempfile.mktemp()
@@ -27,8 +27,8 @@ class ListLikeFileIter:
self._fileIter = iter(self._fileptr.readline,"")
def __del__(self):
@@ -1626,3 +1637,14 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100
- Py_InitModule("halign", registration_table);
+ PyModule_Create(&cModMethods);
}
+--- a/atac-driver/atac.pl
++++ b/atac-driver/atac.pl
+@@ -732,7 +732,7 @@ sub makeChains {
+ #
+ $ENV{'PYTHONPATH'} = "$LIBdir";
+
+- if (runCommand("python $chainer $ATACdir/work/$matches.matches.extended")) {
++ if (runCommand("python3 $chainer $ATACdir/work/$matches.matches.extended")) {
+ print STDERR "PYTHONPATH=$ENV{'PYTHONPATH'}\n";
+ die "Chainer failed.\n";
+ }
=====================================
debian/rules
=====================================
@@ -40,5 +40,8 @@ override_dh_install:
sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' $${perlscript} ; \
done
+override_dh_python3:
+ dh_python3 --no-ext-rename
+
get-orig-source:
DEB_VERSION_UPSTREAM=$(DEB_VERSION_UPSTREAM) debian/get-orig-source
View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/cd6de6e90b30e0fc86f88afdfcc9b6350e05400a...ce9928609f54f4be938797fac6a9f155eb7ad629
--
View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/cd6de6e90b30e0fc86f88afdfcc9b6350e05400a...ce9928609f54f4be938797fac6a9f155eb7ad629
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