TypeError: a bytes-like object is required, not 'str'

[abrozzi]

Dear Ryan,

referred to this klebgenomics/Kaptive#15 (comment):

python SRST2-table-from-assemblies/srst2_table_from_assemblies.py 
--assemblies SRST2-table-from-assemblies/example_data/sample* 
--gene_db SRST2-table-from-assemblies/example_data/gene_db.mfasta 
--output test

gives me the following error:

Traceback (most recent call last):
 File "SRST2-table-from-assemblies/srst2_table_from_assemblies.py", line 335, in <module>
   main()
 File "SRST2-table-from-assemblies/srst2_table_from_assemblies.py", line 52, in main
   blast_results = blast_assembly(assembly, args.gene_db, args.algorithm, unique_allele_symbols)
 File "SRST2-table-from-assemblies/srst2_table_from_assemblies.py", line 164, in blast_assembly
   for line in blast_results_iterator(out):
 File "SRST2-table-from-assemblies/srst2_table_from_assemblies.py", line 255, in blast_results_iterator
   nextnl = results.find('\n', prevnl + 1)
TypeError: a bytes-like object is required, not 'str'

Thank you!
-A

[abrozzi]

Resolved: It works with python2.7.

It crashes with python3.8.

This is because here at line 255:

 http://stackoverflow.com/questions/3054604/iterate-over-the-lines-of-a-string
def blast_results_iterator(results):
    prevnl = -1
    while True:  
      nextnl = results.find('\n', prevnl + 1)
      if nextnl < 0: break
      yield results[prevnl + 1:nextnl]
      prevnl = nextnl

python2.7 and python3.8 treats differently bytes and string.

A possible solution to make it version independent would be to save somewhere the output of blastn and read it as tab separated values table.

my two cents,
Alex

[ronaldgevern]

The reason for this error is that in Python 3, strings are Unicode, but when transmitting on the network, the data needs to be bytes instead. We can convert bytes to string using bytes class decode() instance method, So you need to decode the bytes object to produce a string. In Python 3 , the default encoding is "utf-8" , so you can use directly:

b"python byte to string".decode("utf-8")

Python makes a clear distinction between bytes and strings . Bytes objects contain raw data — a sequence of octets — whereas strings are Unicode sequences . Conversion between these two types is explicit: you encode a string to get bytes, specifying an encoding (which defaults to UTF-8); and you decode bytes to get a string. Clients of these functions should be aware that such conversions may fail, and should consider how failures are handled.

[PaynDita]

a bytes-like object is required not 'str'

simply add .decode()
eg;

If keyword in load:

return load

Error:

if keyword in load:

TypeError: a bytes-like object is required not 'str'

solution:

If keyword in load.decode():

return load

For easy understanding click the below link:
https://payndita.wixsite.com/it-garage/post/a-bytes-like-object-is-required-not-str