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zhangchonglab / CRISPRi-functional-genomics-in-prokaryotes

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finding gRNAs on a single gene #2

Open batflorez opened 4 years ago

batflorez commented 4 years ago

config_mApple2_gRNA_100919.txt first of all, nice tool!. I have been trying to use it to automatically design gRNAs for my experiments (I am not running libraries at the moment). I'm doing a control experiment where I want to find gRNAs for a fluorescent protein (mApple2) so that would be just one gene (see attached). I had to modify the code a bit because I am using python 3, however the analysis runs well but I get the following error:

Design process for mApple2 starts. Copy number: 1 Gene length: 711.0 Command line:./seqmap 5 N20NGGofftarget.fasta NC_022898_PY79.fna seqmapOut.temp.dat /output_all_matches Loading fasta file N20NGGofftarget.fasta. 56 sequences read, total length is 1288. analysing probes...totally 56 probes, minimum length = 23, maximum length = 23, set internal key length = 23 importing probes....56 probes imported. 56 are valid. checking resources...64-bit version. available memory: 8128MB. generating reversed probes for searching reverse strand now 112 probes. 112 are valid. Split probe into 6 parts. total 6 copies of probes. estimated memory usage: 12MB. Building 6 probe lists......6 probe lists created. estimated search speed is 302118 bps/sec. detecting probes .... average search steps:1.08999 maximum search steps:4 4033459 base pairs processed. average search speed: 694514 bps/sec. time used: 17.6061 seconds 4 sgRNA detected for mApple2

cut: mApple2_mNeon.gene_statistics.txt: No such file or directory cut: mApple2_mNeon.sgRNA_statistics.txt: No such file or directory Traceback (most recent call last): File "sgRNA_desgin_main.py", line 348, in main(sys.argv[1]) File "sgRNA_desgin_main.py", line 329, in main processSgRNASequence('%s.N20.fasta.txt'%(varlist['prefix']),'N20_library.csv','w',False) File "sgRNA_desgin_main.py", line 265, in processSgRNASequence with open(N20file,'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'mApple2_mNeon.N20.fasta.txt

That means it is not able to create the gRNA fasta file for some reason. Any ideas?

mApple_mNeon.txt

batflorez commented 4 years ago

Never mind I fixed, I have to avoid using underscores on file names.