tanghaibao/jcvi issues and pull requests

#748 - synteny.py：IndexError: list index out of range

Issue - State: open - Opened by haihao999 9 days ago - 1 comment

#747 - Remove gene pair only if is_self is on

Pull Request - State: closed - Opened by tanghaibao 19 days ago

#746 - Dev

Pull Request - State: closed - Opened by tanghaibao 21 days ago

#745 - Dev

Pull Request - State: closed - Opened by tanghaibao 22 days ago

#744 - Dev

Pull Request - State: closed - Opened by tanghaibao 24 days ago

#743 - Dev

Pull Request - State: closed - Opened by tanghaibao 25 days ago

#742 - Remove label on the chromosome landscape

Issue - State: closed - Opened by AoiKudoh 26 days ago - 2 comments

#741 - Synteny search getting aborted between cacao and grape

Issue - State: closed - Opened by 247nahid about 1 month ago - 3 comments

#740 - Indicate duplication event on synteny plot?

Issue - State: closed - Opened by erika-r-moore about 1 month ago - 2 comments

#739 - Dev

Pull Request - State: closed - Opened by tanghaibao about 1 month ago

#738 - Housekeeping

Pull Request - State: open - Opened by Adamtaranto about 1 month ago - 2 comments

#737 - Fix dists linux

Pull Request - State: closed - Opened by tanghaibao about 1 month ago - 1 comment

#736 - Fix dists

Pull Request - State: closed - Opened by Adamtaranto about 1 month ago - 1 comment
Labels: bug

#735 - AttributeError: 'LayoutLine' object has no attribute 'order'

Issue - State: open - Opened by pk-zhu about 2 months ago - 6 comments

#734 - Add Black formatting action

Pull Request - State: closed - Opened by Adamtaranto about 2 months ago - 1 comment
Labels: github action

#733 - WIP: Add jcvi.graphics.ribbon module

Pull Request - State: closed - Opened by Adamtaranto about 2 months ago - 1 comment

#732 - WIP: Update_packaging

Pull Request - State: closed - Opened by Adamtaranto about 2 months ago - 1 comment

#730 - ValueError: min() arg is an empty sequence

Issue - State: open - Opened by lindonghuia about 2 months ago - 1 comment

#729 - Spelling error

Pull Request - State: closed - Opened by zhangyixing3 about 2 months ago - 1 comment

#728 - What if I want to merge genomes with a single reference genome just like how you do with microsysteny?

Issue - State: closed - Opened by Triiumpher 2 months ago - 4 comments

#727 - Error: some genes in blocks can't be found, please rerun after making sure that bed file agree with simple file

Issue - State: closed - Opened by oddguyeee 2 months ago - 2 comments

#726 - set initial block color to None

Pull Request - State: closed - Opened by tanghaibao 2 months ago

#725 - findfont: Generic family 'sans-serif', and the words in output .pdf file cannot be edited

Issue - State: open - Opened by louisvant 3 months ago - 2 comments

#724 - Support custom alignment blocks in Microsynteny plots

Issue - State: open - Opened by Adamtaranto 3 months ago - 1 comment
Labels: new feature

#723 - Add publish action

Issue - State: closed - Opened by Adamtaranto 3 months ago - 1 comment
Labels: github action

#722 - Update pytest action

Issue - State: open - Opened by Adamtaranto 3 months ago
Labels: github action

#721 - Add formatting action

Issue - State: closed - Opened by Adamtaranto 3 months ago
Labels: github action

#720 - Add format tests for synteny Layout

Issue - State: open - Opened by Adamtaranto 3 months ago
Labels: tests

#719 - Migrate from setuptools

Issue - State: open - Opened by Adamtaranto 3 months ago
Labels: infrastructure

#718 - blocks and blocks.layout file

Issue - State: open - Opened by seikot345 3 months ago - 1 comment

#717 - update init.py

Pull Request - State: closed - Opened by tanghaibao 3 months ago

#716 - 运行jcvi.graphics.landscape stack时mergeBed报错

Issue - State: closed - Opened by zhangrengang 3 months ago - 2 comments

#715 - “synteny.py assemble” obtain too many gene pairs.

Issue - State: closed - Opened by ZhaoHang-bio 4 months ago - 1 comment

#714 - Change color of inversions

Issue - State: closed - Opened by alexzaccaron 4 months ago - 2 comments

#714 - Change color of inversions

Issue - State: closed - Opened by alexzaccaron 4 months ago - 2 comments

#713 - When a species is compared with itself, why are the gene pairs in the result not all the genes?

Issue - State: closed - Opened by Liuxuanzeng 4 months ago - 5 comments

#713 - When a species is compared with itself, why are the gene pairs in the result not all the genes?

Issue - State: closed - Opened by Liuxuanzeng 4 months ago - 5 comments

#712 - How to add a legend in `python -m jcvi.graphics.landscape heatmap`

Issue - State: open - Opened by ltachi11 4 months ago

#712 - How to add a legend in `python -m jcvi.graphics.landscape heatmap`

Issue - State: open - Opened by ltachi11 4 months ago

#711 - Remove noisy warning logs in Shade (thanks @changchuanjun, #710)

Pull Request - State: closed - Opened by tanghaibao 4 months ago

#711 - Remove noisy warning logs in Shade (thanks @changchuanjun, #710)

Pull Request - State: closed - Opened by tanghaibao 4 months ago

#710 - 画图时出现警告信息：WARNING Shade: None found in coordinates, skipping

Issue - State: closed - Opened by changchuanjun 4 months ago - 3 comments

#709 - list index out of range

Issue - State: open - Opened by lindonghuia 4 months ago - 2 comments

#708 - Add must_open()

Pull Request - State: closed - Opened by tanghaibao 5 months ago

#707 - Synteny Pattern

Issue - State: open - Opened by tamim07 5 months ago - 15 comments

#706 - 我在安装jcvi时遇到了这样的问题，请问该如何解决

Issue - State: closed - Opened by aowuawu 5 months ago - 2 comments

#704 - Be smarter about chrZ (#703, thanks @manighanipoor)

Pull Request - State: closed - Opened by tanghaibao 5 months ago

#703 - jcvi.graphics.karyotype: track lables overlap with tracks

Issue - State: closed - Opened by manighanipoor 5 months ago - 3 comments

#702 - some error happen when i run python3 -m jcvi.graphics.karyotype seqids2 layout2

Issue - State: closed - Opened by xxwgdhd 6 months ago - 2 comments

#701 - 画图时报错ValueError: not enough values to unpack (expected 6, got 3)

Issue - State: closed - Opened by changchuanjun 6 months ago - 7 comments

#700 - Dev

Pull Request - State: closed - Opened by tanghaibao 6 months ago

#699 - Syntenty Search error [lastal: can't interpret: BlastTab]

Issue - State: closed - Opened by Artifice120 6 months ago - 2 comments

#698 - Allow bed format to contain browser/track headers

Pull Request - State: closed - Opened by tanghaibao 7 months ago

#697 - MCScan_Macrosynteny visualization-realiazation of the Karyotype figure

Issue - State: closed - Opened by Triiumpher 7 months ago - 3 comments

#696 - 微共线性(Microsynteny)三个及以上物种比对问题

Issue - State: open - Opened by sdhzwpz 7 months ago - 2 comments

#695 - findfont: Generic family 'sans-serif' not found because none of the following families were found: Helvetica

Issue - State: closed - Opened by jjjjccccc 7 months ago - 4 comments

#694 - Fix None path (thanks @jailynai, #693)

Pull Request - State: closed - Opened by tanghaibao 7 months ago

#693 - TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

Issue - State: closed - Opened by jailynai 7 months ago - 1 comment

#692 - Do not keep empty blocks (#690, thanks @Tong-Chen)

Pull Request - State: closed - Opened by tanghaibao 7 months ago

#691 - Add breakpoints()

Pull Request - State: closed - Opened by tanghaibao 7 months ago

#690 - base.py line 34, in make_ranges q, s, t = zip(*ib) -- ValueError: not enough values to unpack (expected 3, got 0)

Issue - State: closed - Opened by Tong-Chen 7 months ago - 2 comments

#689 - converting mummer result coords file to blast file

Issue - State: closed - Opened by xiaoguizz 7 months ago - 6 comments

#688 - Fix array length when chr length < window (thanks @lkulandaivelu, #686)

Pull Request - State: closed - Opened by tanghaibao 7 months ago

#687 - Ignore empty lines in seqids file

Pull Request - State: closed - Opened by tanghaibao 7 months ago

#686 - Genomic landscape error

Issue - State: closed - Opened by lkulandaivelu 7 months ago - 1 comment

#685 - ! LaTeX Error: File `type1ec.sty' not found.

Issue - State: open - Opened by liuqz-bot 7 months ago - 1 comment

#684 - Minor update

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#683 - 报错：Segmentation fault

Issue - State: open - Opened by monica11w 8 months ago

#682 - Remove comment lines while parsing seqids (thanks @Pedicularis1kib, #676)

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#680 - Dev

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#679 - python3 -m jcvi.compara.catalog ortholog这步报错

Issue - State: closed - Opened by Sherry520 8 months ago - 2 comments

#678 - change back to macos-latest

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#677 - Update README and citation section

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#676 - It reported "ERROR Size of `scaffold_19` is empty. Please check"

Issue - State: closed - Opened by YanCheer 8 months ago - 4 comments

#675 - don't make index

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#674 - don't brew install freetype

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#673 - install error of jcvi

Issue - State: closed - Opened by ma2o-3 9 months ago - 2 comments

#672 - Replace super(Class, self) => super()

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#671 - Visualization of DNA-level Collinearity Using Mummer Data

Issue - State: open - Opened by saltyduckegg 9 months ago - 2 comments

#670 - Add --filter sam

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#668 - Add "otsu" method to GRABSEEDS

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#667 - TypeError: expected a sequence of integers or a single integer, got '69.222553'

Issue - State: closed - Opened by karthickbrlab 9 months ago - 9 comments

#666 - Replace percent with % in assembly.kmer

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#665 - Don't update string when notex=True

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#664 - Test ALLMAPS

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#663 - Test GRABSEEDS

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#662 - How to modify picture parameters？如何修改共线性图片的参数（调整字体大小，pdf的大小）

Issue - State: closed - Opened by MR-D-CJ 9 months ago - 2 comments