DEP3

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@debian.org>

Last-Update: Fri, 22 Nov 2019 11:23:44 +0100

--- a/scripts/last-dotplot

+++ b/scripts/last-dotplot

@@ -1,4 +1,4 @@

 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)

     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()

 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 @@

 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 @@

                     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 @@

 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):

     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 @@

 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 @@

 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")

     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 @@

 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

             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 @@