Closed shellywanamaker closed 4 years ago
Hi Shelly - too easy! try putting your input file into the directory where all the script files are and run it using the input file name without path (i.e, just “silo23_all_pro_GO.tab”) Mish
On Sep 14, 2019, at 10:19 PM, Shelly Trigg notifications@github.com wrote:
Hello,
I continue to get the following error thrown by the gomwu_b.pl script and I'm not sure what's going on. Any advice is appreciated, thanks! -Shelly
gomwuStats(input, goDatabase, goAnnotations, goDivision,
perlPath="perl", # replace with full path to perl executable if it is not in your system's PATH already largest=0.1, # a GO category will not be considered if it contains more than this fraction of the total number of genes smallest=5, # a GO category should contain at least this many genes to be considered clusterCutHeight=0.25) # threshold for merging similar gomwu_b: cannot create output dissim0BP/Users/Shelly/Documents/GitHub/OysterSeedProject/analysis/UniprotAnnotations_NetworkAnalysis/ASCA_logNSAFs_FunctionalAnalysis/silo23_all_pro_GO.tab — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/z0on/GO_MWU/issues/4?email_source=notifications&email_token=ABZUHGGPOA4ZDAAKMNZQBGDQJWSVRA5CNFSM4IWY72I2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HLNDSSQ, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZUHGCU5YXW3ZB3ZM6MKDDQJWSVRANCNFSM4IWY72IQ.
Hey Mish, all my input files are in the directory where all the script files are. I'll try removing the path and see if it runs. I also found some formatting discrepancies in my input file (it included column names and there were "; " separating each GO term. Hopefully it works after these changes. Thanks for your quick response!
that error definitely was because the input filename included path, but hey, there always could be other errors as well! :) please don’t hesitate to ask
On Sep 14, 2019, at 10:46 PM, Shelly Trigg notifications@github.com wrote:
Hey Mish, all my input files are in the directory where all the script files are. I'll try removing the path and see if it runs. I also found some formatting discrepancies in my input file (it included column names and there were "; " separating each GO term. Hopefully it works after these changes. Thanks for your quick response!
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/z0on/GO_MWU/issues/4?email_source=notifications&email_token=ABZUHGDMCFS4HK73U3TJDMDQJWVZ5A5CNFSM4IWY72I2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6XIRDI#issuecomment-531531917, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZUHGEUFCKZLI4PVPZN67LQJWVZ5ANCNFSM4IWY72IQ.
it worked! thanks so much!
Hello,
I continue to get the following error thrown by the gomwu_b.pl script and I'm not sure what's going on. Any advice is appreciated, thanks! -Shelly
gomwuStats(input, goDatabase, goAnnotations, goDivision,