[med-svn] [Git][med-team/dnarrange][master] 4 commits: [skip ci] Add upstream/metadata
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Mon May 30 17:32:19 BST 2022
Nilesh Patra pushed to branch master at Debian Med / dnarrange
Commits:
f5f82c81 by Nilesh Patra at 2022-05-29T16:40:11+05:30
[skip ci] Add upstream/metadata
- - - - -
09fd911d by Nilesh Patra at 2022-05-30T22:00:25+05:30
New upstream version 1.5.2
- - - - -
d8340e06 by Nilesh Patra at 2022-05-30T22:00:35+05:30
Update upstream source from tag 'upstream/1.5.2'
Update to upstream version '1.5.2'
with Debian dir 3dcc18067218ce231e29bab4c7ec155d56b5283e
- - - - -
8a3b89a1 by Nilesh Patra at 2022-05-30T22:01:50+05:30
Interim changelog entry
- - - - -
6 changed files:
- − .gitattributes
- README.md
- debian/changelog
- debian/upstream/metadata
- 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
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+dnarrange (1.5.2-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Add upstream/metadata
+ * New upstream version 1.5.2
+
+ -- Nilesh Patra <nilesh at debian.org> Mon, 30 May 2022 22:01:07 +0530
+
dnarrange (1.5.1-1) unstable; urgency=medium
* Initial release (Closes: #1012044)
=====================================
debian/upstream/metadata
=====================================
@@ -1,19 +1,7 @@
-Reference:
- - Author:
- Title:
- Journal:
- Year:
- Volume:
- Number:
- Pages:
- DOI:
- PMID:
- URL:
- eprint:
-Registry:
- - Name: conda:bioconda
- Entry:
- - Name: SciCrunch
- Entry:
- - Name: bio.tools
- Entry:
+---
+Archive: GitHub
+Bug-Database: https://github.com/mcfrith/dnarrange/issues
+Bug-Submit: https://github.com/mcfrith/dnarrange/issues/new
+Changelog: https://github.com/mcfrith/dnarrange/tags
+Repository: https://github.com/mcfrith/dnarrange.git
+Repository-Browse: https://github.com/mcfrith/dnarrange
=====================================
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/-/compare/efe4bbb5965ebaa24339194b59e08b1aa091194a...8a3b89a1a1be5dae52f82f7c987f7f9d334164b4
--
View it on GitLab: https://salsa.debian.org/med-team/dnarrange/-/compare/efe4bbb5965ebaa24339194b59e08b1aa091194a...8a3b89a1a1be5dae52f82f7c987f7f9d334164b4
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