[med-svn] [Git][med-team/dnarrange][upstream] New upstream version 1.5.2

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch upstream at Debian Med / dnarrange


Commits:
09fd911d by Nilesh Patra at 2022-05-30T22:00:25+05:30
New upstream version 1.5.2
- - - - -


4 changed files:

- − .gitattributes
- README.md
- dnarrange
- setup.py


Changes:

=====================================
.gitattributes deleted
=====================================
@@ -1,2 +0,0 @@
-setup.py export-subst
-tests/ export-ignore


=====================================
README.md
=====================================
@@ -1,7 +1,13 @@
 # dnarrange
 
 This is a method to find rearrangements in "long" DNA reads relative
-to a genome sequence.
+to a genome sequence.  It can characterize changes such as chromosome
+shattering, gene conversion, and processed pseudogene insertion.  For
+more details, please see: [A pipeline for complete characterization of
+complex germline rearrangements from long DNA reads][paper].
+
+You can install dnarrange (together with all other software that it
+uses) from [Bioconda][] or [Debian Med][].
 
 ### Step 1: Align the reads to the genome
 
@@ -74,8 +80,7 @@ it requires the latter to be
 This in turn requires the [Python Imaging
 Library](https://pillow.readthedocs.io/) to be installed.
 
-* A useful option is `--rmsk1`, to show repeats, which often cause
-  rearrangements.
+* A useful option is `-a`, to display files of genes, repeats, etc.
 
 Tips for viewing the pictures on a Mac: open the folder in Finder, and
 
@@ -91,6 +96,8 @@ of 2) reads per group:
 
     dnarrange -s3 groups.maf > strict.maf
 
+**If the results are clear enough, you can stop here!**
+
 ### Step 4: Merge each group into a consensus sequence
 
     dnarrange-merge reads.fq myseq.par groups.maf > merged.fa
@@ -265,13 +272,9 @@ genome more slowly-and-carefully (e.g. without repeat-masking).
 you can see them with `dnarrange-merge --help`, and they're described
 at the [lamassemble] site.
 
-## Paper
-
-For more details, please see: [A pipeline for complete
-characterization of complex germline rearrangements from long DNA
-reads][paper] by S Mitsuhashi, S Ohori, et al.
-
 [BED]: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
+[Bioconda]: https://bioconda.github.io/
+[Debian Med]: https://www.debian.org/devel/debian-med/
 [MAFFT]: https://mafft.cbrc.jp/alignment/software/
 [lamassemble]: https://gitlab.com/mcfrith/lamassemble
 [paper]: https://doi.org/10.1186/s13073-020-00762-1


=====================================
dnarrange
=====================================
@@ -401,22 +401,17 @@ def sharedRearrangement(opts, types, alignmentsA, alignmentsB,
                 continue
             isRevAX = alnAX[8]
             isRevAY = alnAY[8]
-            isUpstreamInQueryA = (alnNumAX < alnNumAY)
             for alnNumBY in alnNumsBY:
+                alnBY = alignmentsB[alnNumBY]
                 for alnNumBX in alnNumsBX:
-                    if alnNumBX == alnNumBY:
-                        continue
                     alnBX = alignmentsB[alnNumBX]
-                    alnBY = alignmentsB[alnNumBY]
                     if isRevAY is alnBY[8]:
-                        if (isRevAX is alnBX[8] and
-                            isUpstreamInQueryA is (alnNumBX < alnNumBY) and
+                        if (alnNumBX < alnNumBY and isRevAX is alnBX[8] and
                             isSharedRearrangement(opts,
                                                   alnAX, alnAY, alnBX, alnBY)):
                             return "+"
                     else:
-                        if (isRevAX is not alnBX[8] and
-                            isUpstreamInQueryA is not (alnNumBX < alnNumBY) and
+                        if (alnNumBX > alnNumBY and isRevAX is not alnBX[8] and
                             isSharedRearrangement(opts,
                                                   alnAX, alnAY, alnBX, alnBY)):
                             return "-"


=====================================
setup.py
=====================================
@@ -1,6 +1,6 @@
 import setuptools
 
-commitInfo = " (HEAD -> master, tag: 1.5.1)".strip("( )").split()
+commitInfo = " (HEAD -> master, tag: 1.5.2)".strip("( )").split()
 version = commitInfo[commitInfo.index("tag:") + 1].rstrip(",")
 
 setuptools.setup(



View it on GitLab: https://salsa.debian.org/med-team/dnarrange/-/commit/09fd911da715779e655b168237444f4fb46daac0

-- 
View it on GitLab: https://salsa.debian.org/med-team/dnarrange/-/commit/09fd911da715779e655b168237444f4fb46daac0
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/20220530/c11b273c/attachment-0001.htm>