linsalrob/PhiSpy

Issues

• ValueError: LOCUS line does not contain - at position 75 in date

  #70 opened 2 months ago by tjcu408
  0

• Tuning parameters for possibly missed prophage

  #69 opened 2 months ago by schorlton-bugseq
  0

• Additional testing/validation genomes

  #42 opened 3 months ago by linsalrob
  0

• TypeError: start=x <class 'float'>

  #68 opened 4 months ago by schorlton-bugseq
  0

• Error during processing, no result output - TypeError: expected str, bytes or os.PathLike object, not StringIO

  #67 opened 6 months ago by naturepoker
  2

• output files not created

  #66 opened 8 months ago by oirazoki
  2

• The glibc version is not compatible

  #65 opened 9 months ago by work-liuyang
  1

• Error when sequence ID is too long

  #53 opened 3 years ago by jcmckerral
  5

• conda installation failed

  #62 opened a year ago by dr-joe-wirth
  3

• Parameter to indicate file name prefixes+

  #58 opened a year ago by ireneortega
  1

• pVOG db no longer available

  #61 opened a year ago by raw-lab
  1

• ValueError: Need a Nucleotide or Protein alphabet

  #63 opened a year ago by qianxin-kxy
  1

• "Contig starting with a partial ORF" warning

  #60 opened 2 years ago by EGTortuero
  0

• some problem with position of att site and prophage region

  #59 opened 2 years ago by work-liuyang
  4

• No bases were counted for orf

  #57 opened 2 years ago by simone-pignotti
  1

• Coordinates interpretation

  #56 opened 2 years ago by iferres
  1

• GFF3 File - Include the att sites

  #55 opened 3 years ago by DNADoubleFelix
  0

• prophage fasta file

  #54 opened 3 years ago by mujiezhang
  0

• Huge memory consumption and runtime with NNNNs

  #52 opened 3 years ago by deprekate
  6

• RepeatFinder: NNNNNN

  #51 opened 3 years ago by linsalrob
  0

• phmms option cleanup

  #47 opened 3 years ago by linsalrob
  1

• Unable to finish + excessive RAM usage

  #45 opened 3 years ago by dcarrillouu
  10

• The misc_feature location off by 1

  #48 opened 3 years ago by deprekate
  0

• Not phage function

  #49 opened 3 years ago by pdec
  1

• multi-contigs

  #50 opened 3 years ago by frihaka
  3

• gbk outpout is the same file as gbk input file

  #46 opened 4 years ago by Taalouane
  0

• ValueError: missing molecule_type in annotations

  #43 opened 4 years ago by snehamurthy21
  5

• ValueError: missing molecule_type in annotations

  #44 opened 4 years ago by snehamurthy21
  0

• ValueError: missing molecule_type in annotations

  #41 opened 4 years ago by tauqeer9
  5

• Fixing phmms data use condition

  #39 opened 4 years ago by pdec
  0

• Selecting features measurements

  #36 opened 4 years ago by pdec
  1

• Keep CDS parts in original frame

  #38 opened 4 years ago by pdec
  0

• Write out phage/not phage genbank files

  #37 opened 4 years ago by linsalrob
  0

• Splitting/merging joined features

  #35 opened 4 years ago by pdec
  0

• Fix status score when rank value above the threshold

  #34 opened 4 years ago by pdec
  0

• Mark prophage regions at the end of contigs

  #33 opened 4 years ago by linsalrob
  0

• numpy.core.umath_tests

  #13 opened 4 years ago by linsalrob
  1

• Lower the gene window

  #20 opened 4 years ago by deprekate
  1

• Minor changes and suguestions

  #28 opened 4 years ago by metageni
  1

• Impossible to use training sets kept in other location than INSTALLATION_DIR

  #31 opened 4 years ago by pdec
  1

• ASCI

  #19 opened 4 years ago by bognabognabogna
  2

• repeatfinder breaks with CentOS8

  #29 opened 5 years ago by linsalrob
  0

• Move all command line argument parsing code in PhiSpy.py to the helper_functions.py file

  #24 opened 5 years ago by deprekate
  2

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

  #27 opened 5 years ago by metageni
  0

• Choice of the longest repeats is non-deterministic

  #26 opened 5 years ago by linsalrob
  0

• Output formatting and tempRepeatDNA

  #9 opened 5 years ago by JoeHeffron
  2

• switch randomforest implementation

  #21 opened 5 years ago by deprekate
  1

• Output GFF3

  #17 opened 5 years ago by JFsanchezherrero
  1

• PhiSpy does not support Python 3

  #7 opened 5 years ago by chris-rands
  2

• PhiSpy installation

  #8 opened 5 years ago by JPiy
  0