mjsull/spa_typing

Computational method for finding spa types.

spa_typing's Issues

TypeError: coercing to Unicode: need string or buffer, NoneType found

 python ./get_spa_type.py
Traceback (most recent call last):
  File "./get_spa_type.py", line 211, in <module>
    the_out = findPattern(args.fasta, seqDict, letDict, typeDict, seqLengths)
  File "./get_spa_type.py", line 126, in findPattern
    qDict = fasta_dict(infile)
  File "./get_spa_type.py", line 21, in fasta_dict
    with open(fasta_name) as fh:
TypeError: coercing to Unicode: need string or buffer, NoneType found

python --version
Python 2.7.13

AttributeError: 'itertools._grouper' object has no attribute 'next'

python3 ./get_spa_type.py
Traceback (most recent call last):
  File "./get_spa_type.py", line 210, in <module>
    seqDict, letDict, typeDict, seqLengths = getSpaTypes(args.repeat_file, args.repeat_order_file)
  File "./get_spa_type.py", line 112, in getSpaTypes
    reps_dict = fasta_dict(reps)
  File "./get_spa_type.py", line 24, in fasta_dict
    header = header.next()[1:].strip()
AttributeError: 'itertools._grouper' object has no attribute 'next'

python3 --version
Python 3.6.1

Support *.fasta parameter with tabular output.

I would like to do "get_spa_type.py *.fasta" and get a table

FILENAME       SPA_TYPE
blah1.fa           Y-H-G-F-M-B-L-O t622
blah2.fa          Y-H-G-A-M-B-L-O t623

ImportError: No module named request

Hi I just downloaded this but cannot seem to run it. There seems to be an issue with line 6?

Peters-MacBook-Pro:~ peter$ python /Users/peter/Desktop/spa_typing-master/get_spa_type.py -f /Users/peter/Desktop/M20_0405.fasta
Traceback (most recent call last):
File "/Users/peter/Desktop/spa_typing-master/get_spa_type.py", line 6, in
import urllib.request
ImportError: No module named request
Peters-MacBook-Pro:~ peter$

Any help would be great! Cheers!

P