data.config

### never have in-line comments in this file


#######
## BLAST SETTINGS

[blast]
#Use your email address, please, this is just for NCBI records
Entrez.email = YourEmail@email.com

#The statistcal cutoff for matches
e_value_thresh = 0.000001

# the max number of matches for each blast search
hitlist_size = 10

# define location for blast database, should be local for the moment.
location = remote
#Options [local, remote]

# if location = local, localblastdb path must be absolute path '/'
localblastdb = /shared/localblastdb_meta/


# if location = remote:
#default url_base is ncbi, to run on AWS set url here
#url_base =

# number of cores to use
num_threads = 8


# when to reblast the included sequences
delay = 90

#######
## PHYSCRAPER SETTINGS

[physcraper]
spp_threshold = 3


#This is how much shorter new sequences are allowed to be compared to your original sequence lengths when added to aln. Is used in during the process of adding new seqs as well as removing seq that are too short
seq_len_perc = 0.9

# value that determines how many seq need to be present before the beginning and end of alignment will be trimmed
trim_perc = 0.9

# max length for values to add to aln
max_len = 1.2