[med-svn] [Git][med-team/lastz][master] 2to3 for test scripts, Build-Depends: python3
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 15 14:08:25 BST 2020
Andreas Tille pushed to branch master at Debian Med / lastz
Commits:
264748ed by Andreas Tille at 2020-06-15T15:07:58+02:00
2to3 for test scripts, Build-Depends: python3
- - - - -
2 changed files:
- debian/control
- debian/patches/2to3.patch
Changes:
=====================================
debian/control
=====================================
@@ -3,7 +3,8 @@ Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper-compat (= 13)
+Build-Depends: debhelper-compat (= 13),
+ python3 <!nocheck>
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/lastz
Vcs-Git: https://salsa.debian.org/med-team/lastz.git
=====================================
debian/patches/2to3.patch
=====================================
@@ -31,6 +31,17 @@ Description: 2to3 for test suite
"""
Compare two axt files, reporting differences but ignoring some trivial ones
---------------------------------------------------------------------------
+@@ -36,8 +36,8 @@ def main():
+
+ # compare the files
+
+- axt1 = file(axt1Filename,"rt")
+- axt2 = file(axt2Filename,"rt")
++ axt1 = open(axt1Filename,"rt")
++ axt2 = open(axt2Filename,"rt")
+ different = compare_files(axt1,axt2,sortEm=sortEm)
+ axt1.close()
+ axt2.close()
@@ -56,11 +56,11 @@ def main():
% (axt1Filename,axt2Filename)
@@ -54,6 +65,15 @@ Description: 2to3 for test suite
"""
Build a "hashed sequence index" (hsx) file for a fasta file
-----------------------------------------------------------
+@@ -165,7 +165,7 @@ def main():
+ f = sys.stdin
+ else:
+ try:
+- f = file(fileName,"rt")
++ f = open(fileName,"rt")
+ except IOError:
+ assert (False), "unable to open %s" % fileName
+
@@ -183,26 +183,26 @@ def main():
if (length == 0):
@@ -275,6 +295,15 @@ Description: 2to3 for test suite
"""
Given a list of intervals, mask those bases in the fasta sequence(s).
"""
+@@ -69,7 +69,7 @@ def main():
+
+ # read the intervals
+
+- f = file(intervalsFile,"rt")
++ f = open(intervalsFile,"rt")
+
+ chromToIntervals = {}
+
@@ -130,12 +130,12 @@ def main():
prevEnd = end
if (prevEnd < len(seq)): newSeq += [seq[prevEnd:]]
@@ -298,7 +327,16 @@ Description: 2to3 for test suite
"""
Compare two gfa files, reporting differences but ignoring some trivial ones
---------------------------------------------------------------------------
-@@ -43,12 +43,12 @@ def main():
+@@ -36,19 +36,19 @@ def main():
+
+ # compare the files
+
+- gfa1 = file(gfa1Filename,"rt")
+- gfa2 = file(gfa2Filename,"rt")
++ gfa1 = open(gfa1Filename,"rt")
++ gfa2 = open(gfa2Filename,"rt")
+
+ if (sortEm): (different,lineNum) = compare_unsorted_files(gfa1,gfa2)
else: (different,lineNum) = compare_sorted_files (gfa1,gfa2)
if (different):
@@ -342,7 +380,7 @@ Description: 2to3 for test suite
"""
"Hashed sequence index" (hsx) file reader (for a fasta file)
-------------------------------------------------------------------
-@@ -87,9 +87,9 @@ class HsxFile(object):
+@@ -87,13 +87,13 @@ class HsxFile(object):
else: self.debug = debug
self.open()
@@ -355,6 +393,11 @@ Description: 2to3 for test suite
msBit5 = 0x80 << (4*8)
def open(self):
+- self.file = file(self.fileName,"rb")
++ self.file = open(self.fileName,"rb")
+
+ self.magic = magic = struct.unpack(">L",self.file.read(4))[0]
+ if (magic == HsxFile.magicBig): self.byteOrder = ">" # (big endian)
@@ -168,22 +168,22 @@ class HsxFile(object):
def get_sequence(self,name):
@@ -408,8 +451,9 @@ Description: 2to3 for test suite
if (seqFile == None):
if ("fetch" in self.debug):
- print >>sys.stderr, "[ opening %s]" % seqFileName
+- seqFile = file(seqFileName,"rt")
+ print("[ opening %s]" % seqFileName, file=sys.stderr)
- seqFile = file(seqFileName,"rt")
++ seqFile = open(seqFileName,"rt")
self.fileTable[fileIx] = (seqFileName,seqFile)
if ("fetch" in self.debug):
- print >>sys.stderr, "[ reading from %s:%012X]" \
@@ -463,6 +507,30 @@ Description: 2to3 for test suite
"""
Compare two lav files, reporting differences but ignoring some trivial ones
---------------------------------------------------------------------------
+@@ -31,8 +31,8 @@ def main():
+
+ # compare the files
+
+- lav1 = file(lav1Filename,"rt")
+- lav2 = file(lav2Filename,"rt")
++ lav1 = open(lav1Filename,"rt")
++ lav2 = open(lav2Filename,"rt")
+
+ different = True
+ stanza = None
+@@ -49,9 +49,9 @@ def main():
+ line2 = line2.rstrip()
+
+ if (stanza != None):
+- if (line1 == "}") != (line2 == "}"): break
+- if (line1 == "}") and (line2 == "}"):
+- stanza = None
++ if (line1 == "}") != (line2 == "}"): break
++ if (line1 == "}") and (line2 == "}"):
++ stanza = None
+ continue
+ stanzaIx += 1
+
@@ -79,12 +79,12 @@ def main():
stanzaIx = 0
@@ -561,6 +629,15 @@ Description: 2to3 for test suite
"""
Select a subset of sequences from a fasta file indexed by an hsx file
---------------------------------------------------------------------
+@@ -44,7 +44,7 @@ def main():
+ usage("missing a value in %s=" % arg)
+
+ if (arg == "--names") and (val != None):
+- f = file(val)
++ f = open(val)
+ seqNames += [line.strip() for line in f]
+ f.close()
+ elif (arg == "--nowarn") and (val == None):
@@ -75,11 +75,11 @@ def main():
for name in seqNames:
seq = hsx.get_sequence(name)
@@ -584,7 +661,7 @@ Description: 2to3 for test suite
"""
Convert probabilities to a LASTZ scores file (including quantum scores)
-----------------------------------------------------------------------
-@@ -263,16 +263,16 @@ def main():
+@@ -263,27 +263,27 @@ def main():
##########
if ("debug" in debug):
@@ -606,8 +683,11 @@ Description: 2to3 for test suite
##########
# write quantum code file
-@@ -282,8 +282,8 @@ def main():
- codeF = file(codeName,"wt")
+ ##########
+
+ if (codeName != None):
+- codeF = file(codeName,"wt")
++ codeF = open(codeName,"wt")
for sym in symbols:
p = symProb[sym]
- print >>codeF, "%s\t%s" \
View it on GitLab: https://salsa.debian.org/med-team/lastz/-/commit/264748ed6f68369b8398d175b4d3245c126b6cbc
--
View it on GitLab: https://salsa.debian.org/med-team/lastz/-/commit/264748ed6f68369b8398d175b4d3245c126b6cbc
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