Hi, I encountered such an error! Could you please provide the missing file? Thanks.
Load the assembly pseudochromosomes that have a CRISPR array and a Cas9[¶](http://222.200.186.124:9111/notebooks/IdentifingTracrRNAs.ipynb#Load-the-assembly-pseudochromosomes-that-have-a-CRISPR-array-and-a-Cas9)
chdir("data") # path to the data folder from the git repo
allAssemblies = dict(fasta_index("proteins/All_Cas9-Like-filtered.faa",'fasta'))
erpEXE_Path = "../scripts/Arnold/erpin"
rhoDatabase = "../scripts/Arnold/rho-indep.epn"
casOperons = load(open("pickles/Cas9_Operons.p","rb"))
1
chdir("data") # path to the data folder from the git repo
2
allAssemblies = dict(fasta_index("proteins/All_Cas9-Like-filtered.faa",'fasta'))
3
erpEXE_Path = "../scripts/Arnold/erpin"
4
rhoDatabase = "../scripts/Arnold/rho-indep.epn"
5
casOperons = load(open("pickles/Cas9_Operons.p","rb"))
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-2-923df5d49587> in <module>
1 chdir("data") # path to the data folder from the git repo
----> 2 allAssemblies = dict(fasta_index("proteins/All_Cas9-Like-filtered.faa",'fasta'))
3 erpEXE_Path = "../scripts/Arnold/erpin"
4 rhoDatabase = "../scripts/Arnold/rho-indep.epn"
5 casOperons = load(open("pickles/Cas9_Operons.p","rb"))
~/miniconda3/envs/cas/lib/python3.7/site-packages/Bio/SeqIO/__init__.py in index(filename, format, alphabet, key_function)
978 )
979 return _IndexedSeqFileDict(
--> 980 proxy_class(filename, format, alphabet), key_function, repr, "SeqRecord"
981 )
982
~/miniconda3/envs/cas/lib/python3.7/site-packages/Bio/SeqIO/_index.py in __init__(self, filename, format, alphabet)
195 def __init__(self, filename, format, alphabet):
196 """Initialize the class."""
--> 197 SeqFileRandomAccess.__init__(self, filename, format, alphabet)
198 marker = {
199 "ace": b"CO ",
~/miniconda3/envs/cas/lib/python3.7/site-packages/Bio/SeqIO/_index.py in __init__(self, filename, format, alphabet)
44 def __init__(self, filename, format, alphabet):
45 """Initialize the class."""
---> 46 self._handle = _open_for_random_access(filename)
47 self._alphabet = alphabet
48 self._format = format
~/miniconda3/envs/cas/lib/python3.7/site-packages/Bio/File.py in _open_for_random_access(filename)
132 If the file is gzipped but not BGZF, a specific ValueError is raised.
133 """
--> 134 handle = open(filename, "rb")
135 magic = handle.read(2)
136 handle.seek(0)
FileNotFoundError: [Errno 2] No such file or directory: 'proteins/All_Cas9-Like-filtered.faa'
Hi, I encountered such an error! Could you please provide the missing file? Thanks.