MorrellLAB BAD_Mutations issues

MorrellLAB / BAD_Mutations

Deleterious mutation prediction pipeline

MIT License

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issues

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BUG:

#54 sunshichao0916 closed 3 years ago
3
Compile - include SNP names?

#53 conJUSTover opened 4 years ago
1
Compile Bug - Won't work on test data

#52 conJUSTover opened 4 years ago
5
Dev

#51 TomJKono closed 4 years ago
0
The XML document has moved

#50 hubner-lab opened 4 years ago
2
Fetch only the latest CDS for each species

#49 TomJKono opened 4 years ago
0
Multiple Trees in File

#48 mmckibben opened 4 years ago
6
Fetch XML ParseError

#47 mmckibben closed 5 years ago
5
Dev

#46 TomJKono closed 5 years ago
0
The logistic P value is only valid for the 41 genomes

#45 lilei1 opened 5 years ago
0
BAD_Mutations Incorrectly Back-translates from PASTA

#44 TomJKono closed 7 years ago
1
Doesn't find HyPhy properly

#43 mojaveazure opened 7 years ago
0
Add Logistic Regression to Prediction

#42 TomJKono opened 7 years ago
0
Sanitize sequence names before alignment

#41 TomJKono closed 7 years ago
1
Add Filtering of Species Databases

#40 TomJKono opened 7 years ago
0
Fail nicely when "required" arguments are not specified

#39 TomJKono opened 7 years ago
0
No output written to output dir with silent error

#38 kate-crosby opened 7 years ago
3
makeblastdb

#37 kate-crosby closed 7 years ago
1
Fail gracefully when no BLAST hits

#36 TomJKono closed 8 years ago
1
Add command for dowloading in Mannual

#35 lilei1 closed 8 years ago
1
Off-by-one error in HyPhy script?

#34 TomJKono closed 8 years ago
1
Skip sequences with ambiguous nucleotides

#33 TomJKono closed 8 years ago
1
Compile HyPhy results

#32 TomJKono closed 8 years ago
1
The fields in header of the prediction output file inconsistent with the ones with NOSNP

#31 lilei1 closed 8 years ago
1
Error in the path of the predict step!

#30 lilei1 closed 8 years ago
1
Warning: you may need to install requests if your python don't have this module

#29 lilei1 closed 8 years ago
1
Warnning: Install pasta need specific DendroPy-3.12.3

#28 lilei1 closed 8 years ago
1
run "setup" in MSI, HYPHY and PASTA can not set path automatically

#27 lilei1 opened 8 years ago
1
create new directories

#26 lilei1 closed 8 years ago
1
'Hordeum_vulgare' in below part shoud be 'hordeum_vulgare'

#25 lilei1 closed 8 years ago
1
Clarifying manual text

#24 pmorrell closed 8 years ago
1
Missing Pasta

#23 Aerin13 opened 8 years ago
0
Inconsistant species naming

#22 Aerin13 opened 8 years ago
0
Sanitize Newick trees before copying into output directory

#21 TomJKono closed 8 years ago
2
pasta dies

#20 fayjustin closed 8 years ago
1
JGI Login Broken Again

#19 TomJKono closed 8 years ago
2
empty temporary substitutions file

#18 fayjustin closed 8 years ago
1
Target species not excluded

#17 fayjustin closed 8 years ago
1
Bad fasta parse

#16 fayjustin closed 8 years ago
1
HyPhy path in config file won't generate

#15 Aerin13 opened 8 years ago
1
Installing dependencies error

#14 ChaochihL opened 8 years ago
0
Example setup code doesn't output usable config file

#13 Aerin13 opened 8 years ago
2
Add UMN MSI module instructions to User Manual

#12 TomJKono closed 8 years ago
1
hyphy command not working

#11 fayjustin closed 8 years ago
0
bad path

#10 fayjustin closed 8 years ago
1
Missing sequence in fasta file

#9 fayjustin closed 8 years ago
3
Safer shell options

#8 pmorrell closed 9 years ago
0
Updated README.md text

#7 pmorrell closed 9 years ago
1
BioPython check for fetch

#6 mojaveazure opened 9 years ago
4
Check for required programs in $PATH

#5 TomJKono closed 9 years ago
0