tmp/rename_files_and_reheader.R

In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

df_rename <- data.frame('new_names' = c('NET-49_BL',
                                      'NET-49_TI',
                                      'NET-50_BL',
                                      'NET-50_TI',
                                      'NET-51_BL',
                                      'NET-51_TI',
                                      'NET-52_BL',
                                      'NET-52_TI',
                                      'NET-53_BL',
                                      'NET-53_TI'),

                        'old_names' = c('NET-40_BL',
                                      'NET-40_TI',
                                      'NET-41_BL',
                                      'NET-41_TI',
                                      'NET-42_BL',
                                      'NET-42_TI',
                                      'NET-43_BL',
                                      'NET-43_TI',
                                      'NET-44_BL',
                                      'NET-44_TI')
)
#####
df_rename <- data.frame('new_names' = c('NET-49',
                                        'NET-50',
                                        'NET-51',
                                        'NET-52',
                                        'NET-53'),

                        'old_names' = c('NET-40',
                                        'NET-41',
                                        'NET-42',
                                        'NET-43',
                                        'NET-44')
)
####

path <-  getwd()

for(i in seq(nrow(df_rename))){
  system(paste0('rename ',
         '\'s/',
         df_rename$old_names[i],
         '/', df_rename$new_names[i],
         '/\' ',
         path, '/*'))
}
####
devtools::load_all('/imppc/labs/lplab/share/marc/repos/ergWgsTools')

bams <- list.files('/imppc/labs/lplab/share/marc/insulinomas/processed/hg38/bam/bwa',
                   pattern = '\\.bam$',
                   full.names = T)

out_path <- '/imppc/labs/lplab/share/marc/insulinomas/processed/hg38/bam/bwa/reheader'

for(bam in bams){

  reheaderBam(bam = bam, out_path = out_path)

}

###
#reheader vcf manta
devtools::load_all('/imppc/labs/lplab/share/marc/repos/ergWgsTools')

bcftools <- 'bcftools'

manta_folders <- list.files(getwd(),
                            pattern = "\\_out\\_manta$")

for(manta_folder in manta_folders){

  vcf <- file.path(manta_folder, 'results', 'variants', 'somaticSV.vcf.gz')

  vcf_name <- gsub('_out_manta', '', manta_folder)
  vcf_names <- paste0(vcf_name, c('_BL', '_TI'))

  reheadered_vcf <- file.path(manta_folder, 'somaticSV.vcf.gz')

  bcftoolsReheader(bcftools = bcftools,
                   vcf = vcf,
                   vcf_new_names = vcf_names,
                   reheadered_vcf = reheadered_vcf)
}