phac-nml/sistr_cmd issues and pull requests

#61 - sistr 1.1.3 uses pkg_resource that is deprecated

Issue - State: open - Opened by atks about 1 month ago - 1 comment

#60 - SISTR Release v1.1.3 final merge

Pull Request - State: closed - Opened by kbessonov1984 2 months ago

#59 - SISTR v1.1.3 release

Pull Request - State: closed - Opened by kbessonov1984 2 months ago
Labels: enhancement

#58 - Push v1.1.2 to bioconda?

Issue - State: closed - Opened by russellsmithies 11 months ago - 3 comments

#57 - Discrepant results between similar Salamae genomes

Issue - State: closed - Opened by flashton2003 over 1 year ago - 4 comments

#56 - Question about result output meanings (serovar, serovar antigen, serovar cgmlst)

Issue - State: open - Opened by Dogrinev almost 2 years ago

#55 - Some of Paratyphi A serogroup were assigned as "D1" in SISTR

Issue - State: open - Opened by Wang-Jing-NZ over 2 years ago

#54 - error

Issue - State: closed - Opened by kdyoung100 over 2 years ago - 2 comments

#53 - IndexError: index 0 is out of bounds for axis 0 with size 0

Issue - State: open - Opened by sheikki about 3 years ago - 2 comments

#52 - O51 antigen prediction issues and 35|O51 wzx allele in SISTR v1.1.1 database

Issue - State: open - Opened by kbessonov1984 about 3 years ago

#51 - Updated location of SISTR database URL

Pull Request - State: closed - Opened by apetkau over 3 years ago - 9 comments

#50 - choosing between sistr prediction and refseq match

Issue - State: open - Opened by vappiah over 3 years ago - 1 comment

#49 - Check D1 and D2 serogroup predictions being accurate

Issue - State: open - Opened by kbessonov1984 over 3 years ago
Labels: enhancement

#48 - move EmptyDataError to pandas.errors

Pull Request - State: closed - Opened by jameslz almost 4 years ago - 6 comments

#47 - Galaxy workflow for SISTR v1.1.1 supporting batch processing from raw reads to reports

Pull Request - State: closed - Opened by kbessonov1984 almost 4 years ago - 2 comments
Labels: enhancement

#46 - Serotyping a genome with mixed strains of Salmonella

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

#45 - No reference gnome for SISTR hIT

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

#44 - SISTR v1.1.1 is not compatible with pandas >= 1.1.0 due to failed EmptyDataError exception import

Issue - State: closed - Opened by kbessonov1984 over 4 years ago - 3 comments

#43 - Added blast sorting by bitscore for cgMLST allele calling

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

#42 - Version 1.1.0 or 2.0

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

#41 - "sistr" running time benchmark

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

#40 - Sistr/updates for release

Pull Request - State: closed - Opened by apetkau over 5 years ago - 1 comment

#39 - ImportError: Can't determine version for tables

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

#38 - Add testing coverage for SISTR codebase

Issue - State: open - Opened by jrober84 over 5 years ago

#37 - Doc/database non gitlfs

Pull Request - State: closed - Opened by apetkau over 5 years ago - 1 comment

#36 - Error when mash distance is 1

Issue - State: closed - Opened by Piplopp over 5 years ago - 1 comment

#35 - Sistr cmd update 2018

Pull Request - State: closed - Opened by jrober84 over 5 years ago - 6 comments

#34 - Different cgMLST types depending on version of BLAST

Issue - State: closed - Opened by apetkau about 6 years ago - 15 comments

#33 - Sistr cmd database update 2018

Pull Request - State: closed - Opened by jrober84 about 6 years ago - 3 comments

#32 - Repeated flagellar antigen in both H1 and H2

Issue - State: closed - Opened by jrober84 about 6 years ago

#31 - Duplicated records in fliC DB.

Issue - State: closed - Opened by andersgs about 6 years ago - 1 comment

#30 - problem in wzx.fasta

Issue - State: closed - Opened by alantsangmb about 6 years ago - 2 comments

#29 - contrary wzx wzy predictions

Issue - State: closed - Opened by alantsangmb about 6 years ago - 4 comments

#28 - Wandsbek salamae isolate

Issue - State: closed - Opened by andersgs about 6 years ago - 1 comment

#27 - Better monophasic prediction

Issue - State: closed - Opened by peterk87 over 6 years ago - 1 comment

#26 - sistr_cmd consistently drops one genome from output tables

Issue - State: closed - Opened by sabrinadiemert over 6 years ago - 3 comments

#25 - Decouple SISTR database from sistr_cmd

Issue - State: closed - Opened by peterk87 over 6 years ago - 1 comment

#24 - QC warning if the overall serovar call is to a serovar with less than X number of reference genome representatives

Issue - State: open - Opened by peterk87 almost 7 years ago

#23 - Report number of cgMLST loci found in summary results

Issue - State: closed - Opened by peterk87 almost 7 years ago

#22 - partial H2FljB match

Issue - State: closed - Opened by alantsangmb about 7 years ago - 6 comments

#21 - error：string index out of range

Issue - State: closed - Opened by chen1i6c04 about 7 years ago - 2 comments

#20 - sistr command not recognised

Issue - State: closed - Opened by Papos92 over 7 years ago - 2 comments

#19 - ERROR when using --no-cgmlst

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

#18 - Multiple instances of SISTR on same machine can interfere with each other

Issue - State: closed - Opened by apetkau almost 8 years ago - 4 comments

#17 - ERROR: Missing cgmlst_results

Issue - State: closed - Opened by arif-tanmoy almost 8 years ago - 3 comments

#16 - OSerror when running sistr

Issue - State: closed - Opened by Papos92 almost 8 years ago - 4 comments

#15 - WANTED: Salmonella genomes with trustworthy serovar info!

Issue - State: open - Opened by peterk87 almost 8 years ago - 2 comments
Labels: enhancement, help wanted

#14 - Dev

Pull Request - State: closed - Opened by peterk87 about 8 years ago

#13 - fix #12

Pull Request - State: closed - Opened by peterk87 over 8 years ago

#12 - Which command to use?

Issue - State: closed - Opened by andersgs over 8 years ago - 1 comment

#11 - Pip install does not work

Issue - State: closed - Opened by andersgs over 8 years ago - 2 comments

#10 - which should I select? mash_serovar or serovar?

Issue - State: closed - Opened by JeanGuy777 over 8 years ago - 2 comments

#9 - pip install does not work

Issue - State: closed - Opened by tseemann over 8 years ago - 2 comments

#8 - Tag a release

Issue - State: closed - Opened by tseemann over 8 years ago - 2 comments

#7 - Multiple input file support

Issue - State: closed - Opened by tseemann over 8 years ago - 2 comments
Labels: enhancement

#6 - Create a 'sistr' wrapper script

Issue - State: closed - Opened by tseemann over 8 years ago - 2 comments

#5 - Will you put this in 'pip' ?

Issue - State: closed - Opened by tseemann over 8 years ago - 2 comments
Labels: enhancement

#4 - py2 - INFO: 'DataFrame' object has no attribute 'sort_values'

Issue - State: closed - Opened by tseemann over 8 years ago - 1 comment

#3 - AttributeError: 'NoneType' object has no attribute 'shape'

Issue - State: closed - Opened by tseemann over 8 years ago

#2 - AttributeError: 'dict' object has no attribute 'iteritems'

Issue - State: closed - Opened by tseemann over 8 years ago

#1 - ImportError: No module named 'StringIO'

Issue - State: closed - Opened by tseemann over 8 years ago - 1 comment

GitHub / phac-nml/sistr_cmd issues and pull requests