Where can we get bLactam-PBP_Updater.sh to run SPN_PBP-Gene_Typer.pl

[AlefNeem]

Hi I would like to run this script but one of the script mentioned specifically bLactam-PBP_Updater.sh is missing. Can you upload it as well. Thank you

[BenJamesMetcalf]

Hello,

I'm very sorry for the delay in getting back to you. Over the past few weeks we've been rewriting and testing a new SPN pipeline. In addition to the scripts in the SPN repository there is another repo called 'JanOw_Dependecies' that has 2 more perl scripts (LoTrac_target.pl and PBP-Gene_Typer.pl) that are needed to run the typing software. To be honest this is not an easily exportable program so please let me know if you need any additional assistance.

-Ben

On Fri, Aug 4, 2017 at 10:15 AM AlefNeem notifications@github.com wrote:

Hi I would like to run this script but one of the script mentioned specifically bLactam-PBP_Updater.sh is missing. Can you upload it as well. Thank you

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[btcarlos]

Dear Ben, I am not used to using pipelines, but I have some S. pneumoniae fasta and fastq files from Ion Torrent, with putative new PBP alleles. How can I assign a new number to them? Thanks

[tauqeer9]

Hi Ben I am trying to run PBP-Gene_Typer.pl on a sample and it works well until assembly step, but after that it gives this error- "Use of uninitialized value $pbp_1A in concatenation (.) or string at ./PBP-Gene_Typer.pl line 364." Any help will be appreciated.

Tauqeer

[ksibi]

Hi, I'm facing the same problem and gives the same error "Use of uninitialized value $pbp_1A in concatenation (.) or string at ./PBP-Gene_Typer.pl line 364." could any body help please Thank you Boutheina