R/processQiimeClassifications.R

In felipepratalima/gunga:

# processQiimeClassifications <- function(qiimeClassifications = NULL, taxdumprObject = NULL) {
#   qiimeClassifications$qiimeLineage <- qiimeClassifications$qiimeLineage %>% as.character
#
#   qiimeClassifications$qiimeSuperkingdomName <- str_extract(qiimeClassifications$qiimeLineage, "k__.*?(;|$)")
#   qiimeClassifications$qiimeSuperkingdomName <- str_replace(qiimeClassifications$qiimeSuperkingdomName, "k__", "")
#   qiimeClassifications$qiimeSuperkingdomName <- str_replace(qiimeClassifications$qiimeSuperkingdomName, "\\[", "")
#   qiimeClassifications$qiimeSuperkingdomName <- str_replace(qiimeClassifications$qiimeSuperkingdomName, "\\]", "")
#   qiimeClassifications$qiimeSuperkingdomName <- str_replace(qiimeClassifications$qiimeSuperkingdomName, ";", "")
#   qiimeClassifications$qiimeSuperkingdomName <- ifelse(
#     qiimeClassifications$qiimeSuperkingdomName != "",
#     qiimeClassifications$qiimeSuperkingdomName,
#     NA)
#
#   qiimeClassifications$qiimePhylumName <- str_extract(qiimeClassifications$qiimeLineage, "p__.*?(;|$)")
#   qiimeClassifications$qiimePhylumName <- str_replace(qiimeClassifications$qiimePhylumName, "p__", "")
#   qiimeClassifications$qiimePhylumName <- str_replace(qiimeClassifications$qiimePhylumName, "\\[", "")
#   qiimeClassifications$qiimePhylumName <- str_replace(qiimeClassifications$qiimePhylumName, "\\]", "")
#   qiimeClassifications$qiimePhylumName <- str_replace(qiimeClassifications$qiimePhylumName, ";", "")
#   qiimeClassifications$qiimePhylumName <- ifelse(
#     qiimeClassifications$qiimePhylumName != "",
#     qiimeClassifications$qiimePhylumName,
#     NA)
#
#   qiimeClassifications$qiimeClassName <- str_extract(qiimeClassifications$qiimeLineage, "c__.*?(;|$)")
#   qiimeClassifications$qiimeClassName <- str_replace(qiimeClassifications$qiimeClassName, "c__", "")
#   qiimeClassifications$qiimeClassName <- str_replace(qiimeClassifications$qiimeClassName, "\\[", "")
#   qiimeClassifications$qiimeClassName <- str_replace(qiimeClassifications$qiimeClassName, "\\]", "")
#   qiimeClassifications$qiimeClassName <- str_replace(qiimeClassifications$qiimeClassName, ";", "")
#   qiimeClassifications$qiimeClassName <- ifelse(
#     qiimeClassifications$qiimeClassName != "",
#     qiimeClassifications$qiimeClassName,
#     NA)
#
#   qiimeClassifications$qiimeOrderName <- str_extract(qiimeClassifications$qiimeLineage, "o__.*?(;|$)")
#   qiimeClassifications$qiimeOrderName <- str_replace(qiimeClassifications$qiimeOrderName, "o__", "")
#   qiimeClassifications$qiimeOrderName <- str_replace(qiimeClassifications$qiimeOrderName, "\\[", "")
#   qiimeClassifications$qiimeOrderName <- str_replace(qiimeClassifications$qiimeOrderName, "\\]", "")
#   qiimeClassifications$qiimeOrderName <- str_replace(qiimeClassifications$qiimeOrderName, ";", "")
#   qiimeClassifications$qiimeOrderName <- ifelse(
#     qiimeClassifications$qiimeOrderName != "",
#     qiimeClassifications$qiimeOrderName,
#     NA)
#
#   qiimeClassifications$qiimeFamilyName <- str_extract(qiimeClassifications$qiimeLineage, "f__.*?(;|$)")
#   qiimeClassifications$qiimeFamilyName <- str_replace(qiimeClassifications$qiimeFamilyName, "f__", "")
#   qiimeClassifications$qiimeFamilyName <- str_replace(qiimeClassifications$qiimeFamilyName, "\\[", "")
#   qiimeClassifications$qiimeFamilyName <- str_replace(qiimeClassifications$qiimeFamilyName, "\\]", "")
#   qiimeClassifications$qiimeFamilyName <- str_replace(qiimeClassifications$qiimeFamilyName, ";", "")
#   qiimeClassifications$qiimeFamilyName <- ifelse(
#     qiimeClassifications$qiimeFamilyName != "",
#     qiimeClassifications$qiimeFamilyName,
#     NA)
#
#   qiimeClassifications$qiimeGenusName <- str_extract(qiimeClassifications$qiimeLineage, "g__.*?(;|$)")
#   qiimeClassifications$qiimeGenusName <- str_replace(qiimeClassifications$qiimeGenusName, "g__", "")
#   qiimeClassifications$qiimeGenusName <- str_replace(qiimeClassifications$qiimeGenusName, "\\[", "")
#   qiimeClassifications$qiimeGenusName <- str_replace(qiimeClassifications$qiimeGenusName, "\\]", "")
#   qiimeClassifications$qiimeGenusName <- str_replace(qiimeClassifications$qiimeGenusName, ";", "")
#   qiimeClassifications$qiimeGenusName <- ifelse(
#     qiimeClassifications$qiimeGenusName != "",
#     qiimeClassifications$qiimeGenusName,
#     NA)
#
#   qiimeClassifications$qiimeSpeciesName <- str_extract(qiimeClassifications$qiimeLineage, "s__.*")
#   qiimeClassifications$qiimeSpeciesName <- str_replace(qiimeClassifications$qiimeSpeciesName, "s__", "")
#   qiimeClassifications$qiimeSpeciesName <- str_replace(qiimeClassifications$qiimeSpeciesName, "\\[", "")
#   qiimeClassifications$qiimeSpeciesName <- str_replace(qiimeClassifications$qiimeSpeciesName, "\\]", "")
#   qiimeClassifications$qiimeSpeciesName <- ifelse(
#     qiimeClassifications$qiimeSpeciesName != "",
#     paste(qiimeClassifications$qiimeGenusName, qiimeClassifications$qiimeSpeciesName),
#     NA)
#
#   qiimeClassifications$taxonomyId <-
#     qiimeClassifications$qiimeSpeciesName %>% getTaxonomyIdsByNames(taxdumprObject, .)
#
#   qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>% is.na] <-
#     qiimeClassifications$qiimeGenusName[qiimeClassifications$taxonomyId %>% is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
#
#   qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>% is.na] <-
#     qiimeClassifications$qiimeFamilyName[qiimeClassifications$taxonomyId %>% is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
#
#   qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>% is.na] <-
#     qiimeClassifications$qiimeOrderName[qiimeClassifications$taxonomyId %>% is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
#
#   qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>% is.na] <-
#     qiimeClassifications$qiimeClassName[qiimeClassifications$taxonomyId %>% is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
#
#   qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>% is.na] <-
#     qiimeClassifications$qiimePhylumName[qiimeClassifications$taxonomyId %>% is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
#
#   qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>% is.na] <-
#     qiimeClassifications$qiimeSuperkingdomName[qiimeClassifications$taxonomyId %>% is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
#
#   # Standize Ids
#   standardDf <- getStandardIdsDataFrame(unique(qiimeClassifications$taxonomyId), taxdumprObject)
#   qiimeClassifications <- qiimeClassifications %>% merge(standardDf, by = "taxonomyId")
#
#   # Get complete taxonomy
#   taxonomyDf <- unique(qiimeClassifications$taxonomyId) %>% getStandardLineageIdsAndScientificNamesByIdsAsDataFrame(taxdumprObject, .)
#   qiimeClassifications <- qiimeClassifications %>% merge(taxonomyDf, by = "taxonomyId")
#
#   return(qiimeClassifications)
# }

processQiimeClassifications <- function (qiimeClassifications = NULL, qiimeOtuTable = NULL, taxdumprObject = NULL)
{
  qiimeClassifications$qiimeLineage <- qiimeClassifications$qiimeLineage %>%
    as.character
  qiimeClassifications$qiimeSuperkingdomName <- str_extract(qiimeClassifications$qiimeLineage,
                                                            "k__.*?(;|$)")
  qiimeClassifications$qiimeSuperkingdomName <- str_replace(qiimeClassifications$qiimeSuperkingdomName,
                                                            "k__", "")
  qiimeClassifications$qiimeSuperkingdomName <- str_replace(qiimeClassifications$qiimeSuperkingdomName,
                                                            "\\[", "")
  qiimeClassifications$qiimeSuperkingdomName <- str_replace(qiimeClassifications$qiimeSuperkingdomName,
                                                            "\\]", "")
  qiimeClassifications$qiimeSuperkingdomName <- str_replace(qiimeClassifications$qiimeSuperkingdomName,
                                                            ";", "")
  qiimeClassifications$qiimeSuperkingdomName <- ifelse(qiimeClassifications$qiimeSuperkingdomName !=
                                                         "", qiimeClassifications$qiimeSuperkingdomName, NA)
  qiimeClassifications$qiimePhylumName <- str_extract(qiimeClassifications$qiimeLineage,
                                                      "p__.*?(;|$)")
  qiimeClassifications$qiimePhylumName <- str_replace(qiimeClassifications$qiimePhylumName,
                                                      "p__", "")
  qiimeClassifications$qiimePhylumName <- str_replace(qiimeClassifications$qiimePhylumName,
                                                      "\\[", "")
  qiimeClassifications$qiimePhylumName <- str_replace(qiimeClassifications$qiimePhylumName,
                                                      "\\]", "")
  qiimeClassifications$qiimePhylumName <- str_replace(qiimeClassifications$qiimePhylumName,
                                                      ";", "")
  qiimeClassifications$qiimePhylumName <- ifelse(qiimeClassifications$qiimePhylumName !=
                                                   "", qiimeClassifications$qiimePhylumName, NA)
  qiimeClassifications$qiimeClassName <- str_extract(qiimeClassifications$qiimeLineage,
                                                     "c__.*?(;|$)")
  qiimeClassifications$qiimeClassName <- str_replace(qiimeClassifications$qiimeClassName,
                                                     "c__", "")
  qiimeClassifications$qiimeClassName <- str_replace(qiimeClassifications$qiimeClassName,
                                                     "\\[", "")
  qiimeClassifications$qiimeClassName <- str_replace(qiimeClassifications$qiimeClassName,
                                                     "\\]", "")
  qiimeClassifications$qiimeClassName <- str_replace(qiimeClassifications$qiimeClassName,
                                                     ";", "")
  qiimeClassifications$qiimeClassName <- ifelse(qiimeClassifications$qiimeClassName !=
                                                  "", qiimeClassifications$qiimeClassName, NA)
  qiimeClassifications$qiimeOrderName <- str_extract(qiimeClassifications$qiimeLineage,
                                                     "o__.*?(;|$)")
  qiimeClassifications$qiimeOrderName <- str_replace(qiimeClassifications$qiimeOrderName,
                                                     "o__", "")
  qiimeClassifications$qiimeOrderName <- str_replace(qiimeClassifications$qiimeOrderName,
                                                     "\\[", "")
  qiimeClassifications$qiimeOrderName <- str_replace(qiimeClassifications$qiimeOrderName,
                                                     "\\]", "")
  qiimeClassifications$qiimeOrderName <- str_replace(qiimeClassifications$qiimeOrderName,
                                                     ";", "")
  qiimeClassifications$qiimeOrderName <- ifelse(qiimeClassifications$qiimeOrderName !=
                                                  "", qiimeClassifications$qiimeOrderName, NA)
  qiimeClassifications$qiimeFamilyName <- str_extract(qiimeClassifications$qiimeLineage,
                                                      "f__.*?(;|$)")
  qiimeClassifications$qiimeFamilyName <- str_replace(qiimeClassifications$qiimeFamilyName,
                                                      "f__", "")
  qiimeClassifications$qiimeFamilyName <- str_replace(qiimeClassifications$qiimeFamilyName,
                                                      "\\[", "")
  qiimeClassifications$qiimeFamilyName <- str_replace(qiimeClassifications$qiimeFamilyName,
                                                      "\\]", "")
  qiimeClassifications$qiimeFamilyName <- str_replace(qiimeClassifications$qiimeFamilyName,
                                                      ";", "")
  qiimeClassifications$qiimeFamilyName <- ifelse(qiimeClassifications$qiimeFamilyName !=
                                                   "", qiimeClassifications$qiimeFamilyName, NA)
  qiimeClassifications$qiimeGenusName <- str_extract(qiimeClassifications$qiimeLineage,
                                                     "g__.*?(;|$)")
  qiimeClassifications$qiimeGenusName <- str_replace(qiimeClassifications$qiimeGenusName,
                                                     "g__", "")
  qiimeClassifications$qiimeGenusName <- str_replace(qiimeClassifications$qiimeGenusName,
                                                     "\\[", "")
  qiimeClassifications$qiimeGenusName <- str_replace(qiimeClassifications$qiimeGenusName,
                                                     "\\]", "")
  qiimeClassifications$qiimeGenusName <- str_replace(qiimeClassifications$qiimeGenusName,
                                                     ";", "")
  qiimeClassifications$qiimeGenusName <- ifelse(qiimeClassifications$qiimeGenusName !=
                                                  "", qiimeClassifications$qiimeGenusName, NA)
  qiimeClassifications$qiimeSpeciesName <- str_extract(qiimeClassifications$qiimeLineage,
                                                       "s__.*")
  qiimeClassifications$qiimeSpeciesName <- str_replace(qiimeClassifications$qiimeSpeciesName,
                                                       "s__", "")
  qiimeClassifications$qiimeSpeciesName <- str_replace(qiimeClassifications$qiimeSpeciesName,
                                                       "\\[", "")
  qiimeClassifications$qiimeSpeciesName <- str_replace(qiimeClassifications$qiimeSpeciesName,
                                                       "\\]", "")
  qiimeClassifications$qiimeSpeciesName <- ifelse(qiimeClassifications$qiimeSpeciesName !=
                                                    "", paste(qiimeClassifications$qiimeGenusName, qiimeClassifications$qiimeSpeciesName),
                                                  NA)
  qiimeClassifications$taxonomyId <- qiimeClassifications$qiimeSpeciesName %>%
    getTaxonomyIdsByNames(taxdumprObject, .)
  qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>%
                                    is.na] <- qiimeClassifications$qiimeGenusName[qiimeClassifications$taxonomyId %>%
                                                                                    is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
  qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>%
                                    is.na] <- qiimeClassifications$qiimeFamilyName[qiimeClassifications$taxonomyId %>%
                                                                                     is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
  qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>%
                                    is.na] <- qiimeClassifications$qiimeOrderName[qiimeClassifications$taxonomyId %>%
                                                                                    is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
  qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>%
                                    is.na] <- qiimeClassifications$qiimeClassName[qiimeClassifications$taxonomyId %>%
                                                                                    is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
  qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>%
                                    is.na] <- qiimeClassifications$qiimePhylumName[qiimeClassifications$taxonomyId %>%
                                                                                     is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
  qiimeClassifications$taxonomyId[qiimeClassifications$taxonomyId %>%
                                    is.na] <- qiimeClassifications$qiimeSuperkingdomName[qiimeClassifications$taxonomyId %>%
                                                                                           is.na] %>% getTaxonomyIdsByNames(taxdumprObject, .)
  standardDf <- getStandardIdsDataFrame(unique(qiimeClassifications$taxonomyId),
                                        taxdumprObject)
  qiimeClassifications <- qiimeClassifications %>% merge(standardDf,
                                                         by = "taxonomyId")
  taxonomyDf <- unique(qiimeClassifications$taxonomyId) %>%
    getStandardLineageIdsAndScientificNamesByIdsAsDataFrame(taxdumprObject,
                                                            .)
  qiimeClassifications <- qiimeClassifications %>% merge(taxonomyDf,
                                                         by = "taxonomyId")

  qiimeClassifications <- qiimeClassifications %>% merge(qiimeOtuTable[,1:2], by = "qiimeOtuId")
  return(qiimeClassifications)
}