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kew222 / Self-Targeting-Spacer-Searcher

Set of scripts for finding self-targeting instances in CRISPR arrays
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Troubles with -Accs mode #2

Closed pentamorfico closed 5 years ago

pentamorfico commented 5 years ago

Input: "python2 STSS.py --Accs assemblies.txt" assemblies.txt content: _GCF000005845.2 Output error: """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Traceback (most recent call last): File "STSS.py", line 2764, in sys.exit(main()) File "STSS.py", line 2755, in main protein_list = self_target_search(provided_dir,search,num_limit,E_value_limit,CRT_params,pad_locus,complete_only,skip_PHASTER,percent_reject,default_limit,redownload,current_dir,bin_path,Cas_gene_distance,protein_HMM_file,repeat_HMM_file,prefix,CDD,ask) File "STSS.py", line 2513, in self_target_search CRISPR_results, affected_genomes = spacer_scanner(fastanames,bin_path,CRT_params,current_dir,prefix) UnboundLocalError: local variable 'fastanames' referenced before assignment """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" I tried to run the -Accs mode with RefSeq accession number, GenBank accession number and assembly accession and none of them seems to work. The -search mode runs perfectly. This is a great software, thank you so much for sharing!

kew222 commented 5 years ago

Hi Mario,

It's probably an easy fix, but I'm actually driving/moving to the east coast over the next two weeks to start a new job. I'll try to take a look if I find time, but it may be awhile. I just wanted you to know that I got your email and it's on my radar.

Kyle

On Sat, Nov 24, 2018 at 5:14 AM Mario Rodríguez notifications@github.com wrote:

Input: "python2 STSS.py --Accs assemblies.txt" assemblies.txt content: GCF_000005845.2 Output error:

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Traceback (most recent call last): File "STSS.py", line 2764, in sys.exit(main()) File "STSS.py", line 2755, in main protein_list = self_target_search(provided_dir,search,num_limit,E_value_limit,CRT_params,pad_locus,complete_only,skip_PHASTER,percent_reject,default_limit,redownload,current_dir,bin_path,Cas_gene_distance,protein_HMM_file,repeat_HMM_file,prefix,CDD,ask) File "STSS.py", line 2513, in self_target_search CRISPR_results, affected_genomes = spacer_scanner(fastanames,bin_path,CRT_params,current_dir,prefix) UnboundLocalError: local variable 'fastanames' referenced before assignment

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" I tried to run the -Accs mode with RefSeq accession number, GenBank accession number and assembly accession and none of them seems to work. The -search mode runs perfectly. This is a great software, thank you so much for sharing!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kew222/Self-Targeting-Spacer-Searcher/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AIRGnl3sFzl_lSnX7AZY2YqavM3Pt2_Qks5uyUY5gaJpZM4Yxa8n .

-- Kyle Watters Postdoctoral Associate Doudna Lab, UC Berkeley

kew222 commented 5 years ago

Thanks for pointing out this bug. It looked like I had ported that option over to the deprecated STSS_wrapper.py file. I've set it back up in STSS.py, changed the readme to accurately describe how to use it in the new release (v1.1.0).

Please note that your test assemblies file will still not work however, because I learned awhile back that NCBI's Entrez tools are terrible for going from lists of accessions to uIDs, so you will need to provide the list as uIDs (GCF_000005845.2 -> 79781). However, there are no self-targeting spacers in that genome. I would use uID 330201 (Moraxella bovoculi strain 33362) as a test case (there is a now a results file example for this genome in the repository.

Also, please note that there was a bug where certain complete, single-contig genomes were not being scanned properly immediately after downloading, causing some self-targets to be missed. The bug did not affect genomes that were already downloaded (e.g., given by --dir, or running --search twice). The bug was fixed in the latest release, so you may want to recheck any data you've run.

Sorry this took so long for me to get to.