serulab / py4bio Goto Github PK

  File "muscleserver.py", line 38, in result
    fi_fh.write(sequence)
TypeError: a bytes-like object is required, not 'str'

    % if bad_option:
NameError: name 'bad_option' is not defined

[murphy@eva02 ch4]$ python3 protnetcharge.py 
Enter protein sequence: KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
7.736999999999999
[murphy@eva02 ch4]$ python3 protnetcharge2.py 
  File "protnetcharge2.py", line 8
    nd{verbatim}
      ^
SyntaxError: invalid syntax
[murphy@eva02 ch4]$ cat protnetcharge2.py 
prot_seq = input('Enter protein sequence: ').upper()
charge = -0.002
aa_charge = {'C':-.045,'D':-.999,'E':-.998,'H':.091,
             'K':1,'R':1,'Y':-.001}
for aa in prot_seq:
    charge += aa_charge.get('aa', 0)
print(charge)
nd{verbatim}
[murphy@eva02 ch4]$ vim protnetcharge2.py 
[murphy@eva02 ch4]$ head -n 7 protnetcharge2.py > pnc2.py
[murphy@eva02 ch4]$ tail pnc2.py 
prot_seq = input('Enter protein sequence: ').upper()
charge = -0.002
aa_charge = {'C':-.045,'D':-.999,'E':-.998,'H':.091,
             'K':1,'R':1,'Y':-.001}
for aa in prot_seq:
    charge += aa_charge.get('aa', 0)
print(charge)
[murphy@eva02 ch4]$ python3 pnc2.py 
Enter protein sequence: KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
-0.002

$ ./primer3_core < swforprimer3.txt
...
PRIMER_PRODUCT_SIZE_RANGE=45-57544
PRIMER_ERROR=thermodynamic approach chosen, but path to thermodynamic parameters not specified
=

PRIMER_SEQUENCE_ID={title}
SEQUENCE_TEMPLATE={seq}
TARGET={pos},{win_size}
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=20
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_EXPLAIN_FLAG=1
PRIMER_PRODUCT_SIZE_RANGE={win_size}-{len_seq}
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=primer3-2.4.0/src/primer3_config/
=

[murphy@eva02 ch4]$ python3 seachindict.py 
Traceback (most recent call last):
  File "seachindict.py", line 4, in <module>
    print(color_code[name])
TypeError: list indices must be integers or slices, not str
[murphy@eva02 ch4]$ cat seachindict.py 
color_code = [('red',1), ('green',2), ('blue',3), ('black',4)]
name = 'blue'
color_code_d = dict(color_code)
print(color_code[name])
[murphy@eva02 ch4]$ python
Python 3.7.4 (default, Aug 12 2019, 14:45:07) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> color_code = [('red',1), ('green',2), ('blue',3), ('black',4)]
>>> name = 'blue'
>>> color_code_d = dict(color_code)
>>> print(color_code[name])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: list indices must be integers or slices, not str