mjsull / spa_typing Goto Github PK
View Code? Open in Web Editor NEWComputational method for finding spa types.
Computational method for finding spa types.
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
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
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
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
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