Charles Plessy pushed to branch upstream at Debian Med / last-align
Commits:
2f174580 by Charles Plessy at 2026-07-10T12:06:21+09:00
New upstream version 1652
- - - - -
4 changed files:
- bin/maf-convert
- src/makefile
- test/maf-convert-test.out
- test/maf-convert-test.sh
Changes:
=====================================
bin/maf-convert
=====================================
@@ -1076,11 +1076,20 @@ def writeBlastTab(opts, formatName, geneticCode, maf):
gapOpens, begB, endB, begA, endA]
score, evalue = scoreAndEvalue(aLine)
+
+ bitScore = None
+ if score and opts.bitScoreA is not None and opts.bitScoreB is not None:
+ bitScore = opts.bitScoreA * float(score) - opts.bitScoreB
+ bitScore = "%.3g" % bitScore
+
+ if formatName == "blasttab+":
+ if not evalue: evalue = 'NA'
+ if not bitScore: bitScore = 'NA'
+
if evalue:
out.append(evalue)
- if score and opts.bitScoreA is not None and opts.bitScoreB is not None:
- bitScore = opts.bitScoreA * float(score) - opts.bitScoreB
- out.append("%.3g" % bitScore)
+ if bitScore:
+ out.append(bitScore)
if formatName == "blasttab+":
out += [seqLenB, seqLenA, score]
=====================================
src/makefile
=====================================
@@ -95,7 +95,7 @@ ScoreMatrixData.hh: ../data/*.mat
../build/mat-inc.sh ../data/*.mat > $@
VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1651) ' | sed -e 's/.*tag: *//' -e
's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1652) ' | sed -e 's/.*tag: *//' -e
's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
test/maf-convert-test.out
=====================================
@@ -8349,6 +8349,9 @@ chrUn_KI270748v1 UN-L1PA2_pol#LINE/L1 93.39 227
15 0 3860 4540 1049 1275 1.5e-16
chrUn_KI270748v1 UN-L1MA6_pol#LINE/L1 62.18 386 107 14
3661 2577 518 879 2.5e-152 546 93321 1275 1607.4
chrUn_KI270748v1 UN-L1MA6_pol#LINE/L1 61.64 292 89 8
90089 89272 884 1164 2e-147 530 93321 1275 1559.7
chrUn_KI270748v1 UN-L1PA16_pol#LINE/L1 64.07 359 96 11
17572 18588 527 864 3.8e-142 512 93321 1276 1508.0
+90089 chrX 92.38 656 8 21 49 670 23075590
23076237 NA NA 2478 156040895 3061
+90089 chr7 87.72 114 1 6 776 676 121351143
121351256 NA NA 2478 159345973 493
+90089 chr7 96.82 1699 8 33 2431 777 121348854
121350550 NA NA 2478 159345973 9115
UN-L1MA6_pol#LINE/L1 chrUn_KI270748v1 63.82 633 194 13
658 1273 13905 15715 0 1.08e+03
UN-L1PA2_pol#LINE/L1 chrUn_KI270748v1 93.39 227 15 0
1049 1275 3860 4540 1.5e-169 603
UN-L1MA6_pol#LINE/L1 chrUn_KI270748v1 62.18 386 107 14
518 879 3661 2577 2.5e-152 546
=====================================
test/maf-convert-test.sh
=====================================
@@ -25,6 +25,7 @@ maf2=bs100.maf
$r -l120 blast HERVS71A.maf # test ambiguous N bases
$r blasttab $maf2
$r blasttab+ frameshift-new.maf
+ $r blasttab+ 90089.maf
$r -s2 blasttab frameshift-new.maf
maf-cut DF0000170.5:633-798 herv30.maf | $r blasttab # gaps at edges
maf-cut DF0000170.5:633-798 herv30.maf | $r -s2 blasttab # gaps at edges
View it on GitLab:
https://salsa.debian.org/med-team/last-align/-/commit/2f174580f6dbf28108ae4a295b231ae032e8f9dd
--
View it on GitLab:
https://salsa.debian.org/med-team/last-align/-/commit/2f174580f6dbf28108ae4a295b231ae032e8f9dd
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