genetic_code_examiner.py
Explore potential alternative nuclear genetic codes for input taxa.
genetic_code_examiner.py [OPTIONS] -i <input_file> -q <query_file>
Required arguments:
-i
,--input <infile.fas>
Fasta file with nucleotide sequences-q
,--queries <Unique ID1,Unique ID2,...>
Comma separated Unique IDs of related organisms in the database which should be used as queries.
Optional arguments:
-t
,--threads <N>
Number of threads- Default:
1
- Default:
--prepare_alignments
Prepare alignments for genetic code analysis. MUST BE USED ON THE FIRST RUN!-c
,--conserved <N>
Proportion (0-1) of taxa from the database that have the same amino acid at a position.- Default:
0.7
(70%)
- Default:
-e
,--blast_evalue <1e-X>
E-value threshold for blast searches.- Default:
1e-30
- Default:
-a
,--all_codons
Plot conserved positions for all codons-o
,--output <out_dir>
Path to user-defined output directory- Default:
./genetic_code_out_<M.D.Y>
- Default:
-h
,--help
Show this help message and exit
NOTE: Users should have their config.ini file in the directory in which they wish to run genetic_code_examiner.py
. Users may need to provide updated paths in this file to account for a different directory location.
Default genetic_code_examiner.py
output:
- a file
inputname_genecode.pdf
- Each bar chart in the file corresponds to a separate plot for codons with a suspicious genetic code signal (signal for coding schemes different from the standard nuclear genetic code) if any exist (Figure 8).