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 <[email protected]> +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.
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