[med-svn] [Git][med-team/last-align][master] DEP3

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / last-align


Commits:
da4b75cc by Andreas Tille at 2019-11-22T10:40:54Z
DEP3

- - - - -


1 changed file:

- debian/patches/2to3.patch


Changes:

=====================================
debian/patches/2to3.patch
=====================================
@@ -1,5 +1,8 @@
-diff --git a/scripts/last-dotplot b/scripts/last-dotplot
-index 441cbad..c5199f0 100755
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/943148
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 22 Nov 2019 11:23:44 +0100
+
 --- a/scripts/last-dotplot
 +++ b/scripts/last-dotplot
 @@ -1,4 +1,4 @@
@@ -23,7 +26,7 @@ index 441cbad..c5199f0 100755
  
  def trimmed(seqRanges, coverDict, minAlignedBases, maxGapFrac, endPad, midPad):
      maxEndGapFrac, maxMidGapFrac = twoValuesFromOption(maxGapFrac, ",")
-@@ -308,7 +308,7 @@ def rangesWithStrandInfo(seqRanges, strandOpt, alignments, seqIndex):
+@@ -308,7 +308,7 @@ def rangesWithStrandInfo(seqRanges, stra
  def natural_sort_key(my_string):
      '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
      parts = re.split(r'(\d+)', my_string)
@@ -32,7 +35,7 @@ index 441cbad..c5199f0 100755
      return parts
  
  def nameKey(oneSeqRanges):
-@@ -577,7 +577,7 @@ def drawJoins(im, alignments, bpPerPix, seqIndex, rangeDict1, rangeDict2):
+@@ -577,7 +577,7 @@ def drawJoins(im, alignments, bpPerPix,
  def expandedSeqDict(seqDict):
      '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
      newDict = seqDict.copy()
@@ -50,8 +53,6 @@ index 441cbad..c5199f0 100755
  
  def readGenePred(opts, fileName, rangeDict):
      for line in myOpen(fileName):
-diff --git a/scripts/last-map-probs b/scripts/last-map-probs
-index b05a362..0d133e2 100755
 --- a/scripts/last-map-probs
 +++ b/scripts/last-map-probs
 @@ -1,4 +1,4 @@
@@ -69,8 +70,6 @@ index b05a362..0d133e2 100755
  
  import gzip
  import sys, os, math, optparse, signal
-diff --git a/scripts/last-postmask b/scripts/last-postmask
-index 6ce29a2..eb6d23e 100755
 --- a/scripts/last-postmask
 +++ b/scripts/last-postmask
 @@ -1,4 +1,4 @@
@@ -106,8 +105,6 @@ index 6ce29a2..eb6d23e 100755
                      colHeads = fields[1:]
              elif nf == len(colHeads) + 2 and len(fields[1]) == 1:
                  rowHeads.append(fields[1])
-diff --git a/scripts/last-train b/scripts/last-train
-index 70f71e4..7fd0508 100755
 --- a/scripts/last-train
 +++ b/scripts/last-train
 @@ -1,7 +1,7 @@
@@ -120,7 +117,7 @@ index 70f71e4..7fd0508 100755
  
  import gzip
  import math, optparse, os, random, signal, subprocess, sys, tempfile
-@@ -215,7 +215,7 @@ def writeMatrixWithLetters(outFile, matrix, prefix):
+@@ -215,7 +215,7 @@ def writeMatrixWithLetters(outFile, matr
      writeMatrixBody(outFile, prefix, left, body, "%6s")
  
  def matProbsFromCounts(counts, opts):
@@ -129,8 +126,6 @@ index 70f71e4..7fd0508 100755
      if opts.revsym:  # add complement (reverse strand) substitutions
          counts = [[counts[i][j] + counts[-1-i][-1-j] for j in r] for i in r]
      if opts.matsym:  # symmetrize the substitution matrix
-diff --git a/scripts/maf-convert b/scripts/maf-convert
-index 3225b6d..ac1c895 100755
 --- a/scripts/maf-convert
 +++ b/scripts/maf-convert
 @@ -1,4 +1,4 @@
@@ -148,8 +143,6 @@ index 3225b6d..ac1c895 100755
  
  from itertools import *
  import gzip
-diff --git a/scripts/maf-cut b/scripts/maf-cut
-index 9b9aa69..f21b036 100755
 --- a/scripts/maf-cut
 +++ b/scripts/maf-cut
 @@ -1,6 +1,6 @@
@@ -161,7 +154,7 @@ index 9b9aa69..f21b036 100755
  
  import gzip
  import itertools
-@@ -70,12 +70,12 @@ def cutMafRecords(mafLines, alnBeg, alnEnd):
+@@ -70,12 +70,12 @@ def cutMafRecords(mafLines, alnBeg, alnE
  
  def mafFieldWidths(mafRecords):
      sRecords = (i for i in mafRecords if i[0] == "s")
@@ -177,8 +170,6 @@ index 9b9aa69..f21b036 100755
      print("%*s %-*s %*s %*s %*s %*s %*s" % tuple(formatParams))
  
  def cutOneMaf(cutRange, mafLines):
-diff --git a/scripts/maf-join b/scripts/maf-join
-index 49afca8..d3162a9 100755
 --- a/scripts/maf-join
 +++ b/scripts/maf-join
 @@ -1,4 +1,4 @@
@@ -196,7 +187,7 @@ index 49afca8..d3162a9 100755
  
  import functools
  import sys, os, fileinput, optparse, signal
-@@ -229,7 +229,7 @@ def nextWindow(window, theInput, referenceMaf):
+@@ -229,7 +229,7 @@ def nextWindow(window, theInput, referen
          while True:
              maf = theInput.peek()
              if maf.after(referenceMaf): break
@@ -205,8 +196,6 @@ index 49afca8..d3162a9 100755
              if not maf.before(referenceMaf): yield maf
      except StopIteration: pass
  
-diff --git a/scripts/maf-swap b/scripts/maf-swap
-index f009b26..9b3c930 100755
 --- a/scripts/maf-swap
 +++ b/scripts/maf-swap
 @@ -1,4 +1,4 @@



View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/da4b75cc3adbd1467c7245d23184334f96b4b5d7

-- 
View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/da4b75cc3adbd1467c7245d23184334f96b4b5d7
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20191122/2751053d/attachment-0001.html>