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linsalrob
/
PhiSpy
Prediction of prophages from bacterial genomes
MIT License
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20
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ValueError: LOCUS line does not contain - at position 75 in date
#70
tjcu408
opened
4 weeks ago
0
Tuning parameters for possibly missed prophage
#69
schorlton-bugseq
opened
1 month ago
0
TypeError: start=x <class 'float'>
#68
schorlton-bugseq
opened
2 months ago
0
Error during processing, no result output - TypeError: expected str, bytes or os.PathLike object, not StringIO
#67
naturepoker
opened
5 months ago
2
output files not created
#66
oirazoki
opened
6 months ago
2
The glibc version is not compatible
#65
work-liuyang
opened
8 months ago
1
ValueError: Need a Nucleotide or Protein alphabet
#63
qianxin-kxy
opened
1 year ago
1
conda installation failed
#62
dr-joe-wirth
closed
1 year ago
3
pVOG db no longer available
#61
raw-lab
closed
1 year ago
1
"Contig starting with a partial ORF" warning
#60
EGTortuero
opened
1 year ago
0
some problem with position of att site and prophage region
#59
work-liuyang
opened
2 years ago
4
Parameter to indicate file name prefixes+
#58
ireneortega
closed
1 year ago
1
No bases were counted for orf
#57
simone-pignotti
opened
2 years ago
1
Coordinates interpretation
#56
iferres
closed
2 years ago
1
GFF3 File - Include the att sites
#55
DNADoubleFelix
opened
2 years ago
0
prophage fasta file
#54
mujiezhang
opened
3 years ago
0
Error when sequence ID is too long
#53
jcmckerral
opened
3 years ago
5
Huge memory consumption and runtime with NNNNs
#52
deprekate
closed
3 years ago
6
RepeatFinder: NNNNNN
#51
linsalrob
closed
3 years ago
0
multi-contigs
#50
frihaka
closed
3 years ago
3
Not phage function
#49
pdec
closed
3 years ago
1
The misc_feature location off by 1
#48
deprekate
closed
3 years ago
0
phmms option cleanup
#47
linsalrob
closed
3 years ago
1
gbk outpout is the same file as gbk input file
#46
Taalouane
closed
3 years ago
0
Unable to finish + excessive RAM usage
#45
dcarrillouu
closed
3 years ago
10
ValueError: missing molecule_type in annotations
#44
snehamurthy21
closed
3 years ago
0
ValueError: missing molecule_type in annotations
#43
snehamurthy21
closed
3 years ago
5
Additional testing/validation genomes
#42
linsalrob
closed
1 month ago
0
ValueError: missing molecule_type in annotations
#41
tauqeer9
closed
3 years ago
5
Version 4.2.0
#40
pdec
closed
3 years ago
0
Fixing phmms data use condition
#39
pdec
closed
4 years ago
0
Keep CDS parts in original frame
#38
pdec
closed
4 years ago
0
Write out phage/not phage genbank files
#37
linsalrob
closed
4 years ago
0
Selecting features measurements
#36
pdec
closed
4 years ago
1
Splitting/merging joined features
#35
pdec
closed
4 years ago
0
Fix status score when rank value above the threshold
#34
pdec
closed
4 years ago
0
Mark prophage regions at the end of contigs
#33
linsalrob
opened
4 years ago
0
added code for fasta outputs and cleaned up maketrain
#32
laurasisk
closed
4 years ago
0
Impossible to use training sets kept in other location than INSTALLATION_DIR
#31
pdec
opened
4 years ago
1
Integrated HMM search signal
#30
pdec
closed
4 years ago
0
repeatfinder breaks with CentOS8
#29
linsalrob
closed
4 years ago
0
Minor changes and suguestions
#28
metageni
closed
4 years ago
1
PhiSpy.py: error: unrecognized arguments: -f (update README)
#27
metageni
closed
4 years ago
0
Choice of the longest repeats is non-deterministic
#26
linsalrob
closed
4 years ago
0
Updating master and working
#25
linsalrob
closed
4 years ago
0
Move all command line argument parsing code in PhiSpy.py to the helper_functions.py file
#24
deprekate
closed
4 years ago
2
Automatic preparation of training sets and some minor updates
#23
pdec
closed
4 years ago
0
Fixed error of using wrong variable to set cutoff for min number of genes for a prophage
#22
deprekate
closed
4 years ago
0
switch randomforest implementation
#21
deprekate
closed
4 years ago
1
Lower the gene window
#20
deprekate
closed
4 years ago
1
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