Configuration Files

The configuration files allow you save/restore your settings.

Example file

[Mode]
use_ensembl=yes
use_local_files=no

[Paths]
fasta_directory=/home/$USER/mydir/fa/
loc_directory=/home/$USER/mydir/loc/
grp_file=/home/$USER/mydir/mydir/test.shared_by_all.grp
output_directory=/home/$USER/mydir/ref_out/

[Cleanup]
clean_up_directories=yes

[Run_options]
num_CPU=1

[Penalties]
gap_open_cost=10
gap_extend_cost=0.5
substitution_matrix=EBLOSUM62

[Algorithm]
use_sl_glob=unset
use_sl_ref=yes
use_mx_sum=unset

[Fasta_header]
fasta_header_delimiter=" "
fasta_header_part=0

[Fasta_header]

In case the ids in your loc file are truncated or your fasta headers carry information in addition to the sequence identifier, you can define where to split the fasta header.

Example:

>other:xyz_sequenceID_length:123_species:x
MYQVLQAYDWKYLHDNHDCNFQVGGADQLGNI...

and:

[Fasta_header]
fasta_header_delimiter = "_"
fasta_header_part = 1

Would result in taking only sequenceID into account.

[Run_options]

[Run_options]
num_CPU=1

Will set the maximum number of CPUs to use to one.

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