jaumlrc/ProphET

Issues

• please provide a clean install

  #43 opened 5 years ago by phiweger
  4

• Deprecated database when using ./INSTALL.pl or ./INSTALL.pl --update_db_only

  #40 opened 5 years ago by gkapatai
  2

• gff_rewrite.pl stop in one place and don't move

  #53 opened 2 years ago by nienie123123
  0

• Installation and running

  #52 opened 3 years ago by Songhaoqiu
  0

• INSTALL.pl script error "cat:...No such file or directory"

  #51 opened 3 years ago by rorycave
  0

• Running ProphET against multiple genomes

  #50 opened 3 years ago by JosephWestley
  0

• Regarding attL and attR identification in predicted prophage sequence

  #49 opened 3 years ago by shakti83kumar
  0

• GFF converter not working

  #48 opened 4 years ago by hayleyjaywilson
  0

• Compatibility with Prokka generated GFF using (--compliant) option

  #46 opened 4 years ago by nilesh-tawari
  3

• GFF compatibility (Prooka output --compliant flag)

  #47 opened 4 years ago by nilesh-tawari
  1

• GFF format convert trouble

  #45 opened 4 years ago by PaolaLis8
  0

• Phage genome download from ncbi

  #30 opened 7 years ago by ovpop100
  5

• Unable to find the transcript and gene associated to the CDS

  #44 opened 4 years ago by stefjanson
  2

• Investigate the possibility of taking output of Prokka

  #11 opened 7 years ago by gustavo11
  7

• What tool(s) from EMBOSS do you need?

  #42 opened 5 years ago by tseemann
  0

• Missing description

  #41 opened 5 years ago by tseemann
  0

• Update ProphET_standalone.pl to use RealBin

  #39 opened 5 years ago by microbioticajon
  4

• GFFFile module

  #38 opened 5 years ago by mariemh23
  3

• Corrupt FASTA File during install

  #34 opened 6 years ago by Hana288
  3

• blastall error

  #33 opened 6 years ago by yuq1993
  0

• GFF format trouble

  #20 opened 7 years ago by mariemh23
  21

• Database updating

  #24 opened 7 years ago by kabilov
  3

• Issue near ORI

  #32 opened 7 years ago by gustavo11
  0

• To provide a better description of the files generated

  #12 opened 7 years ago by gustavo11
  1

• Include in TravisCI a test for executions using tRNA as a separate file

  #26 opened 7 years ago by gustavo11
  1

• Consolidate input: both coding sequences and tRNA could only be provided as part of the same GFF file

  #31 opened 7 years ago by gustavo11
  0

• Assign name to predicted phages

  #4 opened 7 years ago by gustavo11
  0

• Output GFFs reporting prophage gene coordinates and annotation

  #6 opened 7 years ago by gustavo11
  0

• obtain_prot_with_annot_seq.pl seems to be unnecessary

  #15 opened 7 years ago by gustavo11
  0

• Improve graph depicting genes, genomes and predicted prophage

  #5 opened 7 years ago by gustavo11
  0

• Adapt application to blast+

  #22 opened 7 years ago by gustavo11
  0

• Some of the log files are being saved in the base directory of execution and later copied to output dir

  #23 opened 7 years ago by gustavo11
  0

• Generate file reporting the day of Prophage database update and stats about that database

  #7 opened 7 years ago by gustavo11
  0

• Github release

  #21 opened 7 years ago by Takadonet
  2

• Consider maintaining a copy of all phage db that were used

  #27 opened 7 years ago by gustavo11
  0

• Travis CI checks should be less stringent

  #25 opened 7 years ago by gustavo11
  1

• Add to each phage db directory a file containing a summary of phage db stats

  #28 opened 7 years ago by gustavo11
  0

• Include in the manual the format of GFF that should be used and how to convert to that format

  #8 opened 7 years ago by gustavo11
  0

• There are two points in the code where STOP codons are discarded. Remove redundancy.

  #18 opened 7 years ago by gustavo11
  1

• Could not find fetch_genomes_based_on_taxid.xml when running INSTALL.pl

  #19 opened 7 years ago by scottdaniel
  1

• Setting up travis CI

  #16 opened 7 years ago by gustavo11
  0

• Installation problems

  #3 opened 7 years ago by nbenzakour
  7

• ABC transporters are not being removed from ProphET database

  #17 opened 7 years ago by gustavo11
  0

• The script is considering part of GFF description as sequence ids

  #9 opened 7 years ago by gustavo11
  0

• Error on line 119 of INSTALL.pl

  #10 opened 7 years ago by gustavo11
  0

• To provide a more extensive description of the prophages found

  #13 opened 7 years ago by gustavo11
  1

• Translate to english comments

  #14 opened 7 years ago by gustavo11
  0