skDooley / TRACR_RNA

8 stars 7 forks source link

No such file or directory: 'proteins/All_Cas9-Like-filtered.faa' #3

Open nongbaoting opened 2 years ago

nongbaoting commented 2 years ago

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'
kushagrasharma commented 2 years ago

Hi Baoting - this file is generated by the first notebook, CRISPR_CasFinding.ipynb. If you run that notebook successfully it'll generate this file.