Reading the code, the blast output is in -outfmt 6 which is tab separated. The code above parses the blast output with | as a separator but the file is actually tab delimited. Another odd thing is that the code extracts the fourth element. I have to confess confusion here, why is the above code working for others?
Anyway I changed the offending line(s) to this:
ref_seq_gb = line.split('\t')[1]
there are two instances where the blast file is parsed.
I am running on MacOS ARM based, the OS is detected correctly as Darwin. Python version 3.9. All deps installed via conda (including blast).
Hi,
Thanks for creating vapid. I'm having a similar problem to issue #14 . However it's on a different line of code:
I am using the default
ref_seq_vir
database. Command I used:I have confirmed all deps are installed (blast, mafft) and running/in path. What's interesting is this line:
This is the output
.blastresults
content:Reading the code, the blast output is in
-outfmt 6
which is tab separated. The code above parses the blast output with|
as a separator but the file is actually tab delimited. Another odd thing is that the code extracts the fourth element. I have to confess confusion here, why is the above code working for others?Anyway I changed the offending line(s) to this:
there are two instances where the blast file is parsed.
I am running on MacOS ARM based, the OS is detected correctly as
Darwin
. Python version 3.9. All deps installed via conda (including blast).