Mercurial > repos > tomnl > mspurity_puritya

annotate combineAnnotations.R @ 0:1251fc5c058e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:11:29 -0400
parents
children 0628c41595e2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
1 library(optparse)
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
2 library(msPurity)
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
3 print(sessionInfo())
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
4
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
5 # Get the parameter
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
6 option_list <- list(
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
7 make_option(c("-s","--sm_resultPth"),type="character"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
8 make_option(c("-m","--metfrag_resultPth"),type="character"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
9 make_option(c("-c","--sirius_csi_resultPth"),type="character"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
10 make_option(c("-p","--probmetab_resultPth"),type="character"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
11 make_option(c("-sw","--sm_weight"),type="numeric"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
12 make_option(c("-mw","--metfrag_weight"),type="numeric"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
13 make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
14 make_option(c("-pw","--probmetab_weight"),type="numeric"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
15 make_option("--create_new_database", action="store_true"),
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
16 make_option(c("-o","--outdir"),type="character", default=".")
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
17 )
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
18 opt <- parse_args(OptionParser(option_list=option_list))
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
19
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
20 print(opt)
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
21
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
22 if (!is.null(opt$create_new_database)){
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
23 sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite')
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
24 file.copy(opt$sm_resultPth, sm_resultPth)
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
25 }else{
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
26 sm_resultPth <- opt$sm_resultPth
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
27 }
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
28
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
29
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
30 weights <-list('sm'=opt$sm_weight,
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
31 'metfrag'=opt$metfrag_weight,
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
32 'sirius_csifingerid'= opt$sirius_csi_weight,
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
33 'probmetab'=opt$probmetab_weight
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
34 )
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
35
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
36 if (round(!sum(unlist(weights),0)==1)){
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
37
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
38 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
39 }
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
40
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
41 summary_output <- msPurity::combineAnnotations(sm_resultPth,
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
42 opt$metfrag_resultPth,
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
43 opt$sirius_csi_resultPth,
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
44 opt$probmetab_resultPth,
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
45 weights = weights)
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
46
1251fc5c058e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
47 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)