mauriceling / bactome Goto Github PK

I think maybe something changed in Fire or there are differences in Python 3, but with the current randomseq.py code, I always get an error AttributeError: 'bool' object has no attribute 'lower'.
Casting it to a string or removing the first part all together since it should be a boolean fixes it.

I suggest changing lines 263 and 265 in randomseq.py to either of the following:

if str(cap_start).lower() == 'true' or cap_start == True:
if str(cap_stop).lower() == 'true' or cap_stop == True:

-or-

if  cap_start == True:
if cap_stop == True:

If you want to see it not working for yourself, launch a fresh Python system by clicking on the launch binder badge here. And then paste the following code in a cell and hit shift-enter to run it.

!pip install fire
!curl -O https://raw.githubusercontent.com/mauriceling/bactome/master/randomseq.py
!python randomseq.py FLS --length=1306 --n=1 --allow_start=True --allow_stop=True

No matter what allow_start and allow_stop are set to, and even if they aren't included, you encounter the error.

Hi,

When using this command:

randomseq.py MS --n=10 --cap_start=False --cap_stop=False --selection="A,250;T,250;G,250;C,250" --fasta=True --statement="c(gtaag);v(10,15,False,False,False,False);c(gtccg);v(20,30,False,False,False,False)",

there is a space between ">" and the sequence name in FASTA header:

e.g.,

> Test_1
gtaagGCAAATACCGCAgtccgTTTCCAGGCTTCACCCGCCAGT
> Test_2
gtaagACGTTCCACGGGAAAgtccgAACTACACTTCCGAACCATATAC
> Test_3
gtaagTGGACGTCCCCAgtccgGCACCCGGACGCAACGGAGAGTTA

Fixed this by changing the code print("> %s" % title) to print(">%s" % title):

>Test_1
gtaagGGTGTCGACATCCgtccgCACCTCTCTCGACAGGTCCTACAGCGA
>Test_2
gtaagGCACCAATCATgtccgGGTCTATTCAAAAAAACCGGA
>Test_3
gtaagTCAAAGAGGGGGgtccgGTCAAGGGAAATACCCCTTCATCTT