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 <[email protected]> Uploaders: Andreas Tille <[email protected]> -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 You're receiving this email because of your account on salsa.debian.org.
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