BUG: about bad_mutations HOT 3 CLOSED

Hello,

Can you tell me more about the environment you are running in? What version of BAD_Mutations are you running? It looks like you may have an outdated version that is expecting different file formats than the ones that are currently supported. Thank you!

from bad_mutations.

Hello Tom,

Thanks for your help. After I changed the format of the subs file, the above error reporting problem was solved.
But now there is a new problem bothering me, the problem is as follows:

For example: There are six amino acid sites mutated in GLYMA_20G250200 sequence, but the final result only shows the last mutation site (aaPos=91) information. Is there any way to output all the mutation site information?
Input sub file:
GLYMA_20G250200.subs
GLYMA_20G250200 635 A 20_47892164
GLYMA_20G250200 482 G 20_47892623
GLYMA_20G250200 447 G 20_47892727
GLYMA_20G250200 300 C 20_47897195
GLYMA_20G250200 278 G 20_47899344
GLYMA_20G250200 91 C 20_47900408

Output result file:
GeneID CDSPos AlignedPosition L0 L1 Constraint Chisquared P-value SeqCount Alignment ReferenceAA MaskedConstraint MaskedP-value LogisticP_Unmasked LogisticP_Masked

GLYMA_20G250200 91 1128 -115.084357697778 -105.3928128322451 0.2211826339688233 19.38308973106581 1.069498940964309e-05 60 ILLLLLLLLLLLIIIIIILLLIILLLSLLLLLLLLLLLLRMMMMMMMMMLLLLLLLLLLI I 0.2214527981159791 1.058092362593577e-05 NA NA

Command line:
./BAD_Mutations.py -v DEBUG compile -P ./Reports -S ./GLYMA_20G250200.subs 2> GLYMA_20G250200.log

log file：
The last line information:
WARNING /vol3/agis/wangli_group/sunshichao/soybean/P101SC17040637-01-F004/bad_mutations/compile_test/Reports/Combined_Report.txt exists! Will overwrite!

Looking forward to your reply, thank you.

Best wish,
Shichao

from bad_mutations.

Hi,
The file feed to -S should be the output file extracted from Annovar output! Not the "./GLYMA_20G250200.subs".
-Li

from bad_mutations.