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.
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