Ecosyste.ms: Issues

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

GitHub / linsalrob/PhiSpy issues and pull requests

#68 - TypeError: start=x <class 'float'>

Issue - State: open - Opened by schorlton-bugseq about 2 months ago

#66 - output files not created

Issue - State: open - Opened by oirazoki 6 months ago - 2 comments

#65 - The glibc version is not compatible

Issue - State: open - Opened by work-liuyang 8 months ago - 1 comment

#63 - ValueError: Need a Nucleotide or Protein alphabet

Issue - State: open - Opened by qianxin-kxy about 1 year ago - 1 comment

#62 - conda installation failed

Issue - State: closed - Opened by dr-joe-wirth about 1 year ago - 3 comments

#61 - pVOG db no longer available

Issue - State: closed - Opened by raw-lab over 1 year ago - 1 comment

#60 - "Contig starting with a partial ORF" warning

Issue - State: open - Opened by EGTortuero over 1 year ago

#59 - some problem with position of att site and prophage region

Issue - State: open - Opened by work-liuyang about 2 years ago - 4 comments

#58 - Parameter to indicate file name prefixes+

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

#57 - No bases were counted for orf

Issue - State: open - Opened by simone-pignotti over 2 years ago - 1 comment

#56 - Coordinates interpretation

Issue - State: closed - Opened by iferres over 2 years ago - 1 comment

#55 - GFF3 File - Include the att sites

Issue - State: open - Opened by DNADoubleFelix over 2 years ago

#54 - prophage fasta file

Issue - State: open - Opened by mujiezhang almost 3 years ago

#53 - Error when sequence ID is too long

Issue - State: open - Opened by jcmckerral about 3 years ago - 5 comments
Labels: help wanted, fix

#52 - Huge memory consumption and runtime with NNNNs

Issue - State: closed - Opened by deprekate about 3 years ago - 6 comments

#51 - RepeatFinder: NNNNNN

Issue - State: closed - Opened by linsalrob about 3 years ago
Labels: enhancement

#50 - multi-contigs

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

#49 - Not phage function

Issue - State: closed - Opened by pdec about 3 years ago - 1 comment
Labels: fix

#48 - The misc_feature location off by 1

Issue - State: closed - Opened by deprekate over 3 years ago

#47 - phmms option cleanup

Issue - State: closed - Opened by linsalrob over 3 years ago - 1 comment
Labels: enhancement, fix

#46 - gbk outpout is the same file as gbk input file

Issue - State: closed - Opened by Taalouane over 3 years ago

#45 - Unable to finish + excessive RAM usage

Issue - State: closed - Opened by dcarrillouu over 3 years ago - 10 comments

#44 - ValueError: missing molecule_type in annotations

Issue - State: closed - Opened by snehamurthy21 over 3 years ago

#43 - ValueError: missing molecule_type in annotations

Issue - State: closed - Opened by snehamurthy21 over 3 years ago - 5 comments
Labels: bug

#42 - Additional testing/validation genomes

Issue - State: closed - Opened by linsalrob almost 4 years ago
Labels: enhancement, help wanted

#41 - ValueError: missing molecule_type in annotations

Issue - State: closed - Opened by tauqeer9 almost 4 years ago - 5 comments
Labels: bug

#40 - Version 4.2.0

Pull Request - State: closed - Opened by pdec almost 4 years ago
Labels: enhancement, fix

#39 - Fixing phmms data use condition

Issue - State: closed - Opened by pdec about 4 years ago
Labels: bug

#38 - Keep CDS parts in original frame

Issue - State: closed - Opened by pdec about 4 years ago
Labels: bug

#37 - Write out phage/not phage genbank files

Issue - State: closed - Opened by linsalrob about 4 years ago
Labels: enhancement

#36 - Selecting features measurements

Issue - State: closed - Opened by pdec about 4 years ago - 1 comment
Labels: enhancement, question

#35 - Splitting/merging joined features

Issue - State: closed - Opened by pdec about 4 years ago
Labels: bug

#34 - Fix status score when rank value above the threshold

Issue - State: closed - Opened by pdec about 4 years ago
Labels: bug

#33 - Mark prophage regions at the end of contigs

Issue - State: open - Opened by linsalrob about 4 years ago
Labels: enhancement

#32 - added code for fasta outputs and cleaned up maketrain

Pull Request - State: closed - Opened by laurasisk about 4 years ago

#31 - Impossible to use training sets kept in other location than INSTALLATION_DIR

Issue - State: open - Opened by pdec about 4 years ago - 1 comment
Labels: enhancement

#30 - Integrated HMM search signal

Pull Request - State: closed - Opened by pdec over 4 years ago
Labels: enhancement, fix

#29 - repeatfinder breaks with CentOS8

Issue - State: closed - Opened by linsalrob over 4 years ago

#28 - Minor changes and suguestions

Issue - State: closed - Opened by metageni over 4 years ago - 1 comment

#27 - PhiSpy.py: error: unrecognized arguments: -f (update README)

Issue - State: closed - Opened by metageni over 4 years ago

#26 - Choice of the longest repeats is non-deterministic

Issue - State: closed - Opened by linsalrob over 4 years ago

#25 - Updating master and working

Pull Request - State: closed - Opened by linsalrob over 4 years ago

#23 - Automatic preparation of training sets and some minor updates

Pull Request - State: closed - Opened by pdec over 4 years ago
Labels: enhancement

#22 - Fixed error of using wrong variable to set cutoff for min number of genes for a prophage

Pull Request - State: closed - Opened by deprekate over 4 years ago
Labels: fix

#21 - switch randomforest implementation

Issue - State: closed - Opened by deprekate over 4 years ago - 1 comment

#20 - Lower the gene window

Issue - State: closed - Opened by deprekate over 4 years ago - 1 comment

#19 - ASCI

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

#18 - Ready for v3.4

Pull Request - State: closed - Opened by pdec over 4 years ago - 1 comment

#17 - Output GFF3

Issue - State: closed - Opened by JFsanchezherrero over 4 years ago - 1 comment

#16 - Fixing ShannonSlope calculation and updating phage kmers lists

Pull Request - State: closed - Opened by pdec over 4 years ago

#15 - PR to complete the update process

Pull Request - State: closed - Opened by linsalrob almost 5 years ago - 1 comment

#14 - Get new Working Repo

Pull Request - State: closed - Opened by linsalrob almost 5 years ago

#13 - numpy.core.umath_tests

Issue - State: closed - Opened by linsalrob almost 5 years ago - 1 comment

#12 - Fixed code and added make_train_set

Pull Request - State: closed - Opened by deprekate almost 5 years ago

#11 - Working

Pull Request - State: closed - Opened by deprekate almost 5 years ago

#10 - Updated code to Python3

Pull Request - State: closed - Opened by deprekate almost 5 years ago - 2 comments

#9 - Output formatting and tempRepeatDNA

Issue - State: closed - Opened by JoeHeffron almost 5 years ago - 2 comments

#8 - PhiSpy installation

Issue - State: closed - Opened by JPiy over 5 years ago

#7 - PhiSpy does not support Python 3

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

#6 - Output

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

#5 - bug report

Issue - State: closed - Opened by HaidYi over 6 years ago

#4 - output files

Issue - State: closed - Opened by ovpop100 over 6 years ago

#3 - i made a singularity container

Pull Request - State: closed - Opened by scottdaniel over 6 years ago - 1 comment

#2 - Added data directory

Pull Request - State: closed - Opened by deprekate over 7 years ago

#1 - Build Failure

Issue - State: closed - Opened by xiaoyunpang almost 8 years ago - 1 comment