Fix the remaining Python3 issues in test scripts

smalt (0.7.6-9) UNRELEASED; urgency=medium

smalt (0.7.6-9) unstable; urgency=medium

  * Team upload.

  [ Andreas Tille ]

  * Use 2to3 to port to Python3

    Closes: #938501

  * debhelper-compat 12

  * Use secure URI in Homepage field.

  * Set upstream metadata fields: Archive, Bug-Submit.

  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g

  TODO: Fix some Python3 issues in test scripts

   make  check-TESTS

   make[4]: Entering directory '/build/smalt-0.7.6/test'

   PASS: splitReads_test.py

   PASS: results_split_test.py

   PASS: ouform_cigar_test.py

   mappings don't match for read 'SIM_000000000_MAL11_001337747_10_F_75m/1'

   FAIL: sample_test.py

   PASS: cigar_test.py

   Discrepancy:

   cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75

   cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75

   cigA1.mapq=60 > MAPQ_THRESH=6 and cigB1.mapq=60 > MAPQ_THRESH=6

   FAIL: mthread_test.py

   PASS: ioform_test.py

   PASS: xali_test.py

   Traceback (most recent call last):

     File "./bam_cigar_test.py", line 254, in <module>

       isOK = testSAMfilesAreIdentical(sambamnam, samoufilnam)

     File "./bam_cigar_test.py", line 149, in testSAMfilesAreIdentical

       linA = infilA.readline()

     File "/usr/lib/python3.7/codecs.py", line 322, in decode

       (result, consumed) = self._buffer_decode(data, self.errors, final)

   UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 366: invalid start byte

   FAIL: bam_cigar_test.py

   =================================

   3 of 9 tests failed

   Please report to hp3@sanger.ac.uk

   =================================

 -- Andreas Tille <tille@debian.org>  Thu, 05 Sep 2019 15:07:37 +0200

  [ Michael R. Crusoe ]

  * Fix some Python3 issues in test scripts

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 03 Jan 2020 11:44:39 +0100

smalt (0.7.6-8) unstable; urgency=medium

Package: smalt-examples

Architecture: all

Depends: ${shlibs:Depends},

         ${misc:Depends}

Depends: ${misc:Depends}

Description: Sequence Mapping and Alignment Tool (examples)

 SMALT efficiently aligns DNA sequencing reads with a reference genome.

 Reads from a wide range of sequencing platforms, for example Illumina,

Author: Andreas Tille <tille@debian.org>

Last-Update: Thu, 05 Sep 2019 15:07:37 +0200

--- a/misc/SAM.py

+++ b/misc/SAM.py

@@ -85,7 +85,7 @@ class Sam:

--- smalt.orig/misc/SAM.py

+++ smalt/misc/SAM.py

@@ -85,7 +85,7 @@

                         self.tags[tagnam] = (typ, fld)

             self.ok = True

         else:

             self.blank()

     def clip(self):

@@ -106,7 +106,7 @@ class Sam:

@@ -106,7 +106,7 @@

         return (typ, isCorrect, s, e)

     def strand(self):

         return bool(self.flag & Sam.FLAG_STRAND)

     def calcUnclippedStart(self):

@@ -207,7 +207,7 @@ class Sam:

@@ -207,7 +207,7 @@

         if  bool(self.flag & Sam.FLAG_STRAND):

             (seq, qual, okflg) = self.reverseComplement()

             if not okflg:

               exit(1)

         else:

             seq = self.nt

@@ -218,7 +218,7 @@ class Sam:

@@ -218,7 +218,7 @@

     def asFastq(self, clip=0):

         namstr, seq, qual = self.asFastqStr()

         if clip >= len(self.nt):

         return Sam.FASTQ_FORMAT % (namstr, seq[clip:], qual[clip:])

     def reverseComplement(self):

@@ -245,7 +245,7 @@ class Sam:

@@ -245,7 +245,7 @@

             if not lin: break

             self.parse(lin, is_verbose)

             if self.ok: break

         return not lin # True if EOF

@@ -259,7 +259,7 @@ def fetchNextRead(infil, read):

@@ -259,7 +259,7 @@

             break

         read.parse(lin)

         if not read.ok:

             continue

         break

         #print read.target.varnum()

@@ -291,8 +291,8 @@ def fetchNextPair(infil, samA, samB):

@@ -291,8 +291,8 @@

                     errflg = True

             if errflg:

                 exit(1)

     return (isEOF, switch_flag)

@@ -307,7 +307,7 @@ def openFile(filnam, mode):

@@ -307,7 +307,7 @@

         else:

             oufil = open(filnam, mode)

     except:

         exit(1)

     return oufil

@@ -316,7 +316,7 @@ if __name__ == '__main__':

@@ -316,7 +316,7 @@

     from sys import argv, exit

     if len(argv) < 3:

         exit(1)

     infilnam = argv[1]

@@ -360,36 +360,36 @@ if __name__ == '__main__':

@@ -360,36 +360,36 @@

                             if mnam == old_qnam:

                                 if read.rname != old_rnam:

                                     chimictr = chimictr + 1

+        print("There were no reads mapped as pairs.")

     exit(0)

--- a/test/bam_cigar_test.py

+++ b/test/bam_cigar_test.py

@@ -164,19 +164,19 @@ def testSAMfilesAreIdentical(filnamA, fi

--- smalt.orig/test/bam_cigar_test.py

+++ smalt/test/bam_cigar_test.py

@@ -142,30 +142,30 @@

 def testSAMfilesAreIdentical(filnamA, filnamB):

     from testdata import openFile

-    infilA = openFile(filnamA)

-    infilB = openFile(filnamB)

+    infilA = openFile(filnamA, 'rb')

+    infilB = openFile(filnamB, 'rb')

     while 1:

         linA = infilA.readline()

-        if not linA or linA[0]!="@":

+        if not linA or linA[0]!= 64:  # same as b"@"

             break

     while 1:

         linB = infilB.readline()

-        if not linB or linB[0]!="@":

+        if not linB or linB[0]!= 64:  # same as b"@"

             break

     okflg = False

     while linA and linB:

-        fldA = linA.split('\t')

-        fldB = linB.split('\t')

+        fldA = linA.split(b'\t')

+        fldB = linB.split(b'\t')

         okflg = len(fldA) == len(fldB)

         if not okflg:

+                  (linA.strip(), linB.strip()))

             break

-        for i in SAM_TEST_FIELDS.keys():

+        for i in list(SAM_TEST_FIELDS.keys()):

             okflg = fldA[i] == fldB[i]

             if not okflg and i == 0:

                 # samtools-0.1.18 view -h produces non-printing char

         for i in SAM_TEST_FIELDS.keys():

@@ -175,8 +175,8 @@

                 # directly after header

                 okflg = fldA[i][1:] == fldB[i] or fldA[i] == fldB[i][1:]

             if not okflg:

                 break       

         if not okflg:

             break

--- a/test/formats.py

+++ b/test/formats.py

@@ -45,9 +45,9 @@ class Cigar:

--- smalt.orig/test/formats.py

+++ smalt/test/formats.py

@@ -24,6 +24,7 @@

 #                                                                           #

 #############################################################################

 #############################################################################

+from operator import ne

 class Cigar:

     from re import compile

@@ -45,9 +46,9 @@

             self.parse(lin)

             okflg = self.ok

             if Cigar.DEBUG:

         return isEOF

     def parse(self, lin):

@@ -66,11 +66,11 @@ class Cigar:

@@ -66,11 +67,11 @@

             self.cigar.strip()

             self.ok = True

             if Cigar.DEBUG:

             self._blank()

     def getMateNo(self):

@@ -118,10 +118,10 @@ def getNextCigarPair(infil, cigA, cigB,

@@ -101,6 +102,15 @@

         if rv: return rv

         return cmp(other.sseg[1], self.sseg[1])

+

+    def __ne__(self, other):

+        rv = ne(self.snam, other.snam)

+        if rv: return rv

+        

+        rv = ne(self.sseg[0], other.sseg[0])

+        if rv: return rv

+

+        return ne(other.sseg[1], self.sseg[1])

 def getNextCigarPair(infil, cigA, cigB, mateno_check = True):

     isOk = False

@@ -118,10 +128,10 @@

         isOk = True

     if not isEOF and mateno_check:

         if cigA.qnam[-2] != cigB.qnam[-2]:

             isOk = False

     return (isOk, isEOF)

@@ -151,6 +151,6 @@ if __name__ == "__main__":

@@ -151,6 +161,6 @@

     infil = openFile(argv[1])

     while not cig.next(infil):

+        print(cig.qnam)

     infil.close()

--- a/test/mthread_test.py

+++ b/test/mthread_test.py

@@ -57,12 +57,12 @@ def cmpCigarFiles(cigfilA, cigfilB, is_v

--- smalt.orig/test/mthread_test.py

+++ smalt/test/mthread_test.py

@@ -57,12 +57,12 @@

             break

         if cigA1 != cigB1:

             if is_verbose:

             if cigA2.mapq > MAPQ_THRESH and cigB2.mapq > MAPQ_THRESH:

                 exit("Discrepancy:\n%s\n%s" % (cigA2.lin, cigB2.lin))

         ctr = ctr + 1

@@ -93,7 +93,7 @@ if __name__ == '__main__':

@@ -93,7 +93,7 @@

     isOK, pairctr = cmpCigarFiles(oufilnam_ref, oufilnam_thread, VERBOSE)

     if VERBOSE:

     if not isOK or pairctr != n_pairs_expected:

         exit("Using smalt in multi-threaded mode gave inconsistent results!")

--- a/test/results_split_test.py

+++ b/test/results_split_test.py

@@ -35,7 +35,7 @@ READSEQS = ("@SIM_000000000_contig5121_0

--- smalt.orig/test/results_split_test.py

+++ smalt/test/results_split_test.py

@@ -35,7 +35,7 @@

             "AAAAGAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAA\n"\

             "+\n"\

             "daBZddeYdBfe`fBf`ecfdfcf`c\eacXdbLe^b``ccadK]e]^_T"\

             )

 # cigar:S:16 SIM_000000000_contig5121_000000001_5120_R_20m/1 20 1 - contig5121 1 20 + 20 M 20

--- a/test/splitReads_test.py

+++ b/test/splitReads_test.py

@@ -79,13 +79,13 @@ def checkOutput(cigfilnam, expected_tup)

--- smalt.orig/test/splitReads_test.py

+++ smalt/test/splitReads_test.py

@@ -79,13 +79,13 @@

     while not cig.next(infil):

         if linctr > n_tup:

             allok = False

             allok = False

             break

@@ -94,7 +94,7 @@ def checkOutput(cigfilnam, expected_tup)

@@ -94,7 +94,7 @@

     for i in range(n_tup):

         if not okflgs[i]:

             allok = False

     if not allok:

--- a/test/testdata.py

+++ b/test/testdata.py

@@ -62,7 +62,7 @@ class DataFiles:

--- smalt.orig/test/testdata.py

+++ smalt/test/testdata.py

@@ -62,7 +62,7 @@

         if len(filnam) < 4 or filnam[-3:] != '.gz': fn_from = fn_from + '.gz'

         fn_to = path.join(DataFiles.WORKDIR, filnam)

         infil = openFile(fn_from, 'r')

         self.logfil_out.write("unpacking '%s' -> '%s'\n" % (fn_from, fn_to))

         while 1:

             lin = infil.readline()

@@ -139,9 +139,9 @@ class DataFiles:

@@ -139,9 +139,9 @@

         for filnam in (self.datafiles + self.tmpfiles):

             if access(filnam, F_OK):

                 remove(filnam)

         self.datafiles = []

         self.tmpfiles = []

         try:

@@ -159,7 +159,7 @@ def openFile(filnam, mode = 'r'):

@@ -159,7 +159,7 @@

         else:

             oufil = open(filnam, mode)

     except:

         exit(1)

     return oufil

--- a/test/sample_test.py

+++ b/test/sample_test.py

--- smalt.orig/test/sample_test.py

+++ smalt/test/sample_test.py

@@ -1,5 +1,7 @@

 # test sampling of insert lengths

 PROGNAM = "../src/smalt"

 REF_FASTA_NAME = "genome_1.fa.gz"

 READ_PREFIX = "gen1l75i300e0"

@@ -105,10 +107,10 @@ def compare_mapping(oufilnam1, oufilnam2

@@ -105,12 +107,12 @@

             break

         ctr2 = ctr2 + 1

             exit("readnames don't match: '%s' vs '%s'" % \

                  (cig1.qnam, cig2.qnam))

-        if cmp(cig1,cig2) and cig1.mapq > 5 and cig2.mapq > 5:

-            exit("mappings don't match for read '%s'" % \

-                 cig1.qnam)

+        if ne(cig1,cig2) and cig1.mapq > 5 and cig2.mapq > 5:

             exit("mappings don't match for read '%s'" % \

                  cig1.qnam)

+            exit("mappings don't match for read '{}'; cig1: {}, cig2: {}, sig1.mapq: {}, sig2.mapq: {}".format(

+                 cig1.qnam, cig1, cig2, cig1.mapq, cig2.mapq))

     infil2.close()

     infil1.close()

        #python $tst

        #rm -f smalt_Xali_test

    else

        python $tst

        python3 $tst

    fi

done