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v 0.1.5.1#45

Merged
HannahBioI merged 101 commits intoBIONF:fdog_goes_assemblyfrom
HannahBioI:fdog-assembly
Jun 13, 2024
Merged

v 0.1.5.1#45
HannahBioI merged 101 commits intoBIONF:fdog_goes_assemblyfrom
HannahBioI:fdog-assembly

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@HannahBioI HannahBioI commented Jun 13, 2024

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trvinh added 30 commits March 15, 2022 14:19
@trvinh
fdogs accepts dots in seed filename
a0747e0
@trvinh
removed fdog assembly files
20aa839
@trvinh
fixed addTaxon replacing pipe
d8eea1f
@trvinh
0.1.0 (BIONF#26)
055051f 
* create v0.1.0

* simplfying hamstr.pl

* first python conversion

* modified addTaxon and addTaxa

* added install/check dependencies

* rename data folders

* added runtime for core complilation
@trvinh
updated README
dd9a45c
@trvinh
fixed kimura distance devide by 0
8624f7d
@trvinh
added preparation runtime to fdogs.run
f984b26
@trvinh
fix path to refspec fa; add amino to hmmbuild
e728252
@trvinh
save core jobs for fdogs.run to file
2405698
@trvinh
speed up preparation in fdogs.run
9edaf9e
@trvinh
fix bug identify seed ID with reuseCore
8332690
@trvinh
reduce evalue for identify seed ID
8855db4
@trvinh
version bump
1edad42
@trvinh
sort hmm hits using domain scores; correct tree walking; setup force …
206def0 
…not delete data; correct profile output with fasOff
@trvinh
sort hmm hits using domain scores; correct tree walking; setup force …
ad2cbbd 
…not delete data; correct profile output with fasOff
@trvinh
v0.1.5 version bump
ad8741d
@trvinh
added fn desc
bfbc324
@trvinh
accept old folder names
4339bad
@trvinh
add option to update json file to checkData
198393d
@trvinh
option to use different names for data folders
ab5491b
@trvinh
add several options to work with data paths
7c3191a
@trvinh
add several options to work with data paths; resolves: BIONF#28
8bd2359
@trvinh
add several options to work with data paths; resolves: BIONF#28
bb185a3
@trvinh
fix sorting hmm hits
5785980
@trvinh
fix check for pathconfig file
f7c4cf8
@trvinh
fix number of hmmhits core compilation
03c9038
@trvinh
rename log fdogs.run
7798d15
@trvinh
adapt evalue
56995b1
@trvinh
adapt evalue
7e6bfbc
@trvinh
muscle5,checkBlast,ignoreAnnoCheck
052cf70
HannahBioI and others added 29 commits February 6, 2024 10:06
@HannahBioI
add function to output only best isoform
6f5dc45
@HannahBioI
Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly
65e5881 
 into fdog-assembly

# Conflicts:
#	fdog/fDOGassembly.py
@HannahBioI
added function to only output one isoform
a33e054
@HannahBioI
new gff function, fixed problem that muscle can not work with path co…
45895c7 
…ntaining @ sysmbols, adapted mergeOutput that merges files with _og ending
@HannahBioI
Merge branch 'BIONF:master' into fdog-assembly
43a2481
@HannahBioI
Fixed bug where fDOG-Assembly does not terminate if FAS raises an error
4e945f9
@HannahBioI
bugfix createGff function
517ca79
@HannahBioI
bugfix createGff function
4670b53
@trvinh
fixed search taxa list when using --coreTaxa
91edb37
@HannahBioI
bugfix gff output
ca892b4
@HannahBioI
Merge branch 'BIONF:master' into fdog-assembly
6fd1b84
@HannahBioI
Merge branch 'fdog_goes_assembly' into fdog-assembly
e8335ec
@HannahBioI
remove MetaEuk tmp files
b52f3ab
@HannahBioI
Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly
c30ab90 
 into fdog-assembly
@trvinh
fixed bug identical geneIDs btw search and refspec
1b4a778
@HannahBioI
bug fix during distance calculation: AS U (selenocystein) will be sco…
863d1d9 
…red as C (cystein)
@HannahBioI
bug fix user output
56930a8
@HannahBioI
Merge branch 'BIONF:master' into fdog-assembly
d47995f
@HannahBioI
Merge branch 'fdog_goes_assembly' into fdog-assembly
06e7b8e
@HannahBioI
bug fix debug mode
3a84185
@HannahBioI
Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly
55e0e9b 
 into fdog-assembly
@HannahBioI
updated check_ref_spec function
d392588
@HannahBioI
updated check_ref_spec function, added region output if augustus is used
7ba1d62
@HannahBioI
update get_distance_function
a5beb17
@HannahBioI
bug fix check_ref_spec function
84e014d
@HannahBioI
v 0.1.5.1
6844790
@HannahBioI
update output containing candidate regions
4d3266d
@HannahBioI
bugfix
2dfbf1b
@HannahBioI
Merge branch 'fdog_goes_assembly' into fdog-assembly
9ae4ef5
@HannahBioI HannahBioI merged commit dddd57a into BIONF:fdog_goes_assembly Jun 13, 2024
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2 participants

@HannahBioI @trvinh