Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / tanghaibao/jcvi issues and pull requests

#545 - Add checks to jcvi.compara.catalog ortholog before running LAST

Issue - State: closed - Opened by Adamtaranto about 2 years ago - 7 comments

#544 - --iter=1 key error

Issue - State: closed - Opened by SAMANDOLL about 2 years ago - 2 comments

#543 - jcvi.compara.catalog ortholog latex ERROR `type1cm.sty' not found

Issue - State: closed - Opened by renmiaozhen about 2 years ago - 3 comments

#542 - jcvi.graphics.karyotype layout error

Issue - State: closed - Opened by cutykaka about 2 years ago

#541 - jcvi.assembly.geneticmap breakpoint with MSTmap

Issue - State: closed - Opened by wyim-pgl about 2 years ago - 2 comments

#540 - Whether each square represents a gene？

Issue - State: closed - Opened by xiaoguizz about 2 years ago - 1 comment

#539 - compara catalog.py error

Issue - State: closed - Opened by ABDULLAHGUJJAR about 2 years ago - 3 comments

#537 - Rotation

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#536 - Attempting to run the example given but got 0 Anchors found

Issue - State: closed - Opened by Wongolini about 2 years ago - 4 comments

#535 - Add option --chrstyle to karyotype

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#534 - many chromosomes inversion, is it true ？

Issue - State: closed - Opened by guo-cheng about 2 years ago - 2 comments

#533 - Parsing error for *cds_from_genomic.fna.gz from NCBI's Genome database

Issue - State: closed - Opened by gunjanpandey about 2 years ago - 3 comments

#532 - Why chromosome ID is not displayed completely ？

Issue - State: closed - Opened by guo-cheng about 2 years ago - 1 comment

#531 - question in jcvi.assembly.kmer

Issue - State: closed - Opened by xingjianfeng100 about 2 years ago - 1 comment

#530 - graphics.synteny 如何更改染色体之间线的粗细和颜色

Issue - State: closed - Opened by shuazhenyang about 2 years ago - 4 comments

#529 - Stringency

Issue - State: open - Opened by jonnyPizza about 2 years ago

#528 - Remove unused deps

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#527 - Update MANIFEST.in

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#526 - Remove version in setup.cfg

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#525 - Remove ALLMAPS deps (thanks @RNieuwenhuis, #522)

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#524 - Remove file shredder

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#523 - Support CrossMap in ALLMAPS (thanks @RNieuwenhuis, #522)

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#522 - liftOver exits with error 255 in subprocess.CalledProcessError

Issue - State: closed - Opened by RNieuwenhuis about 2 years ago - 4 comments

#521 - Integer overflow faSize

Issue - State: closed - Opened by RNieuwenhuis about 2 years ago - 3 comments

#520 - Fix option conflicts

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#519 - TypeError: not all arguments converted during string formatting

Issue - State: closed - Opened by RNieuwenhuis about 2 years ago - 2 comments

#518 - Interpretation of Tandem files

Issue - State: closed - Opened by fafuyyk about 2 years ago - 2 comments

#517 - Downloaded all previous version when install with pip

Issue - State: closed - Opened by xunsheng about 2 years ago - 1 comment

#516 - Add --seed in graphics options

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#515 - jcvi.graphics.dotplot ERROR

Issue - State: closed - Opened by francicco about 2 years ago - 13 comments

#514 - jcvi.assembly.allmaps path ERROR

Issue - State: closed - Opened by francicco about 2 years ago - 1 comment

#513 - Can MCScan be used to detect orthologous gene?

Issue - State: closed - Opened by gouwei1 about 2 years ago - 4 comments

#512 - jcvi.compara.catalog ortholog Error.

Issue - State: closed - Opened by francicco about 2 years ago - 5 comments

#511 - ValueError: A total of 0 anchor was found——compare human with Distant species

Issue - State: closed - Opened by MR-D-CJ over 2 years ago - 4 comments

#510 - just pip install jcvi (thanks @scottcain, #509)

Pull Request - State: closed - Opened by tanghaibao over 2 years ago

#509 - docker build error, "Connection timed out"

Issue - State: closed - Opened by scottcain over 2 years ago - 3 comments

#508 - Plot TEs in MCScan microsynteny ?

Issue - State: closed - Opened by amvarani over 2 years ago - 3 comments

#507 - MCScan dotplot grid

Issue - State: closed - Opened by kfuku52 over 2 years ago - 2 comments

#506 - MCScan microsynteny comparisons between multiple species

Issue - State: closed - Opened by sjfleck over 2 years ago - 5 comments

#505 - Change remove_if_exists() => cleanup()

Pull Request - State: closed - Opened by tanghaibao over 2 years ago

#503 - Recycling of outputs

Issue - State: closed - Opened by mrmrwinter over 2 years ago - 4 comments

#501 - jcvi.graphics.karyotype file output name

Issue - State: closed - Opened by tanghaibao over 2 years ago

#500 - Resources for macrosynteny plot customisation

Issue - State: open - Opened by mrmrwinter over 2 years ago - 4 comments
Labels: new feature, graphics

#498 - Cnv validate wes vs wgs

Pull Request - State: closed - Opened by tanghaibao over 2 years ago

#497 - How to conduct microsynteny for three genomes?

Issue - State: closed - Opened by clementmo over 2 years ago

#496 - Check None first

Pull Request - State: closed - Opened by tanghaibao over 2 years ago

#495 - Fix issue #494 (thanks @LQHHHHH)

Pull Request - State: closed - Opened by tanghaibao over 2 years ago

#494 - Report a problem about pad.py

Issue - State: closed - Opened by LQHHHHH over 2 years ago - 2 comments

#493 - Unable to install

Issue - State: closed - Opened by TommySalvetti01 over 2 years ago - 2 comments

#491 - Allmaps chromosome patch colours bug fix

Pull Request - State: closed - Opened by jguppy over 2 years ago

#490 - Allmaps chromosome patch colours bug

Issue - State: closed - Opened by jguppy over 2 years ago - 2 comments
Labels: bug

#489 - issue with latex was not able to process the following string: b'lp'

Issue - State: closed - Opened by yanhaidong1 over 2 years ago - 7 comments

#486 - Can't convert genbank file to gff file

Issue - State: closed - Opened by chen1i6c04 over 2 years ago

#482 - Unexpected result using --iter==1

Issue - State: closed - Opened by hui-liu over 2 years ago - 6 comments

#481 - Questions about macrosynteny visualization

Issue - State: closed - Opened by Youpu-Chen over 2 years ago - 2 comments

#479 - how to plot duplication result from iter=2?

Issue - State: closed - Opened by zhidaobuzhidao over 2 years ago - 9 comments

#469 - The problem with drawing with the old MCscanX

Issue - State: closed - Opened by Wenwen012345 almost 3 years ago - 1 comment

#466 - The difference between rectangle and roundangle chromosome？

Issue - State: closed - Opened by sunriseTM almost 3 years ago - 1 comment

#465 - IndexError: list index out of range

Issue - State: closed - Opened by xiehui1991 almost 3 years ago - 2 comments

#462 - Can color be set as a hexadecimal color code？(eg: #C7E6F6)

Issue - State: closed - Opened by kuangzhuoran almost 3 years ago - 1 comment

#460 - An error with blast.py and base.py

Issue - State: closed - Opened by wook2014 almost 3 years ago - 2 comments

#452 - python -m jcvi.formats.gff fixpartials cost huge memory.

Issue - State: closed - Opened by xiekunwhy almost 3 years ago - 1 comment

#447 - MANUAL

Issue - State: closed - Opened by somnya almost 3 years ago - 4 comments

#444 - FileNotFoundError: missing font metrics file: phvr7t

Issue - State: closed - Opened by jiangxiuhan0310 almost 3 years ago - 2 comments

#441 - faSize: cannot execute binary file

Issue - State: closed - Opened by aaronphillips7493 about 3 years ago - 2 comments

#433 - jcvi.graphics.karyotype画图没有染色体信息

Issue - State: open - Opened by zxy1555847 about 3 years ago - 3 comments

#425 - How to use MCScanX's result in jcvi?

Issue - State: closed - Opened by phil622 about 3 years ago - 2 comments

#405 - How to get .anchors file without same query gene in one block just like .collinearity file from old version MCScanX

Issue - State: closed - Opened by yanyew over 3 years ago - 8 comments
Labels: TODO, algorithm

#402 - Using this workflow for a new genome

Issue - State: closed - Opened by ardy20 over 3 years ago - 9 comments

#401 - MCscan (Python version) with few genes

Issue - State: closed - Opened by Jacky749 over 3 years ago - 1 comment

#396 - Use closely related genomes to further scaffolding genome

Issue - State: closed - Opened by yplee614 over 3 years ago - 1 comment

#391 - Can ALLMAPS be used to lift Scaffold annotations back down to Contigs?

Issue - State: closed - Opened by aaronphillips7493 over 3 years ago - 1 comment

#389 - No such file or directory: '.bed' (jcvi.compara.catalog ortholog)

Issue - State: closed - Opened by mcsimenc over 3 years ago - 3 comments

#379 - microsynteny plot mixed genes from different species with the same chr name

Issue - State: closed - Opened by obenno over 3 years ago - 1 comment

#368 - MatplotlibDeprecationWarning and missing font metrics file:phvr7t

Issue - State: closed - Opened by LHXqwq almost 4 years ago - 7 comments

#355 - Switch to using JGI REST API

Issue - State: open - Opened by tanghaibao about 4 years ago - 1 comment
Labels: backlog, help needed

#339 - How to add telomere points on chromsomes?

Issue - State: closed - Opened by AlexWanghaoming about 4 years ago - 2 comments
Labels: help needed, new feature

#333 - Cannot change style and font when using jcvi.graphics.synteny

Issue - State: closed - Opened by xieduo7 about 4 years ago - 2 comments
Labels: help needed

#316 - Can different collinear blocks present in different colors in the dotplot?

Issue - State: closed - Opened by xieyichun50 over 4 years ago - 4 comments

#277 - how can i highlight genome duplications?

Issue - State: closed - Opened by niuhuifei over 4 years ago - 6 comments

#244 - Can I use jcvi to plot the MCSCanX

Issue - State: closed - Opened by wuxiaopei0509 almost 5 years ago - 8 comments

#171 - personalization on Macrosynteny visualization

Issue - State: closed - Opened by HippoYI over 5 years ago - 2 comments
Labels: help needed

#120 - ALLMAPS - KeyError: 'C531'

Issue - State: closed - Opened by xiaoshenyin almost 6 years ago - 1 comment

#90 - Unable to create the PDF file (LaTeX issue?)

Issue - State: closed - Opened by UFZZhao about 7 years ago - 4 comments

#60 - low number of ortholog pairs reported

Issue - State: closed - Opened by MichelMoser over 7 years ago - 5 comments

#50 - Script for drawing gene model synteny?

Issue - State: closed - Opened by nextgenusfs almost 8 years ago - 15 comments

#7 - allmaps path failing

Issue - State: closed - Opened by coreywischmeyer almost 9 years ago - 10 comments
Labels: backlog