comparison coral_multilocus_genotype.R @ 8:33d759858625 draft

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7:bcb28b49b0cc

mlg.filter(genind_clone, distance=bitwise_distance) <- 0.032;

# Create list of MLGs.
cat("\nCreating list of mlg_ids...\n\n");
mlg_ids <- mlg.id(genind_clone);

# Read user's Affymetrix 96 well plate tabular file.
affy_metadata_data_frame <- read.table(opt$input_affy_metadata, header=FALSE, stringsAsFactors=FALSE, sep="\t", na.strings=c("", "NA"), quote="");
colnames(affy_metadata_data_frame) <- c("user_specimen_id", "field_call", "bcoral_genet_id", "bsym_genet_id", "reef",
                                        "region", "latitude", "longitude", "geographic_origin", "colony_location",
                                        "depth", "disease_resist", "bleach_resist", "mortality","tle",
                                        "spawning", "collector_last_name", "collector_first_name", "organization", "collection_date",
                                        "email", "seq_facility", "array_version", "public", "public_after_date",

    group_by(row_number()) %>%
    dplyr::rename(group="row_number()") %>%
    unnest (affy_id) %>%
    # Join with mlg table.
    left_join(smlg_data_frame %>%
              select("affy_id","coral_mlg_clonal_id", "coral_mlg_rep_sample_id"),
              by="affy_id");

# If found in database, group members on previous mlg id.
uniques <- unique(sample_mlg_tibble[c("group", "coral_mlg_clonal_id")]);
uniques <- uniques[!is.na(uniques$coral_mlg_clonal_id),];

# A.palmata                  1104
prep_genotype_tibble <- id_data_table %>%
    group_by(row_number()) %>%
    dplyr::rename(group='row_number()') %>%
    unnest(affy_id) %>%
    left_join(smlg_data_frame %>%
        select("affy_id", "coral_mlg_rep_sample_id", "coral_mlg_clonal_id", "user_specimen_id",
               "genetic_coral_species_call", "bcoral_genet_id"),
        by='affy_id');
# Confirm that the representative mlg is the same between runs.
uniques2 <- unique(prep_genotype_tibble[c("group", "coral_mlg_rep_sample_id")]);
uniques2 <- uniques2[!is.na(uniques2$coral_mlg_rep_sample_id),];
na.mlg3 <- which(is.na(prep_genotype_tibble$coral_mlg_rep_sample_id));
na.group2 <- prep_genotype_tibble$group[na.mlg3];

# a100000-… 13905             HG0048           13905
# genetic_coral_species_call bcoral_genet_id
# <chr>                      <chr>
# A.palmata                  C1651
representative_mlg_tibble <- prep_genotype_tibble %>%
    mutate(coral_mlg_rep_sample_id=ifelse(is.na(coral_mlg_rep_sample_id), affy_id, coral_mlg_rep_sample_id)) %>%
    ungroup() %>%
    select(-group);
# prep_genotype_table_tibble looks like this:
# affy_id       coral_mlg_clonal_id user_specimen_id db_match
# a550962...CEL HG0120              1090             match
# genetic_coral_species_call coral_mlg_rep_sample_id
# A.palmata                  1104

# genetic_coral_species_call coral_mlg_rep_sample_id bcoral_genet_id
# A.palmata                  1104                    <NA>
genotype_table_tibble <- prep_genotype_table_tibble %>%
    left_join(affy_metadata_data_frame %>%
        select("user_specimen_id", "bcoral_genet_id"),
        by='user_specimen_id');
write_data_frame(output_data_dir, "genotype.tabular", genotype_table_tibble);

# Output the file needed for populating the person table.
person_table_data_frame <- data.frame(matrix(ncol=4, nrow=num_rows));
colnames(person_table_data_frame) <- c("last_name", "first_name", "organization", "email");

8:33d759858625

mlg.filter(genind_clone, distance=bitwise_distance) <- 0.032;

# Create list of MLGs.
cat("\nCreating list of mlg_ids...\n\n");
mlg_ids <- mlg.id(genind_clone);
cat("\nCreated list of mlg_ids...\n\n");

# Read user's Affymetrix 96 well plate tabular file.
cat("\nCreating affy_metadata_data_frame...\n\n");
affy_metadata_data_frame <- read.table(opt$input_affy_metadata, header=FALSE, stringsAsFactors=FALSE, sep="\t", na.strings=c("", "NA"), quote="");
cat("\nCreated affy_metadata_data_frame...\n\n");
colnames(affy_metadata_data_frame) <- c("user_specimen_id", "field_call", "bcoral_genet_id", "bsym_genet_id", "reef",
                                        "region", "latitude", "longitude", "geographic_origin", "colony_location",
                                        "depth", "disease_resist", "bleach_resist", "mortality","tle",
                                        "spawning", "collector_last_name", "collector_first_name", "organization", "collection_date",
                                        "email", "seq_facility", "array_version", "public", "public_after_date",

    group_by(row_number()) %>%
    dplyr::rename(group="row_number()") %>%
    unnest (affy_id) %>%
    # Join with mlg table.
    left_join(smlg_data_frame %>%
              select("affy_id","coral_mlg_clonal_id", "coral_mlg_rep_sample_id",
                     "genetic_coral_species_call", "bcoral_genet_id"),
              by="affy_id");

# If found in database, group members on previous mlg id.
uniques <- unique(sample_mlg_tibble[c("group", "coral_mlg_clonal_id")]);
uniques <- uniques[!is.na(uniques$coral_mlg_clonal_id),];

# A.palmata                  1104
prep_genotype_tibble <- id_data_table %>%
    group_by(row_number()) %>%
    dplyr::rename(group='row_number()') %>%
    unnest(affy_id) %>%
    left_join(sample_mlg_match_tibble %>%
        select("affy_id", "coral_mlg_rep_sample_id", "coral_mlg_clonal_id",
               "genetic_coral_species_call", "bcoral_genet_id", "db_match"),
        by='affy_id') %>%
    right_join(sample_mlg_match_tibble %>%
        select("coral_mlg_rep_sample_id", "coral_mlg_clonal_id"),
        by='coral_mlg_clonal_id') %>%
        mutate(coral_mlg_rep_sample_id=ifelse(is.na(coral_mlg_rep_sample_id.x),coral_mlg_rep_sample_id.y,coral_mlg_rep_sample_id.x)) %>%
    ungroup() %>%
    dplyr::select(-coral_mlg_rep_sample_id.x,-coral_mlg_rep_sample_id.y, -group.x,-group.y) %>%
    distinct();

# Confirm that the representative mlg is the same between runs.
uniques2 <- unique(prep_genotype_tibble[c("group", "coral_mlg_rep_sample_id")]);
uniques2 <- uniques2[!is.na(uniques2$coral_mlg_rep_sample_id),];
na.mlg3 <- which(is.na(prep_genotype_tibble$coral_mlg_rep_sample_id));
na.group2 <- prep_genotype_tibble$group[na.mlg3];

# a100000-… 13905             HG0048           13905
# genetic_coral_species_call bcoral_genet_id
# <chr>                      <chr>
# A.palmata                  C1651
representative_mlg_tibble <- prep_genotype_tibble %>%
    mutate(coral_mlg_rep_sample_id=ifelse(is.na(coral_mlg_rep_sample_id) & (db_match =="no_match"), affy_id, coral_mlg_rep_sample_id)) %>%
    ungroup() %>%
    select(-group)%>%
    distinct();
# prep_genotype_table_tibble looks like this:
# affy_id       coral_mlg_clonal_id user_specimen_id db_match
# a550962...CEL HG0120              1090             match
# genetic_coral_species_call coral_mlg_rep_sample_id
# A.palmata                  1104

# genetic_coral_species_call coral_mlg_rep_sample_id bcoral_genet_id
# A.palmata                  1104                    <NA>
genotype_table_tibble <- prep_genotype_table_tibble %>%
    left_join(affy_metadata_data_frame %>%
        select("user_specimen_id", "bcoral_genet_id"),
        by='user_specimen_id') %>%
    drop_na(coral_mlg_rep_sample_id);
write_data_frame(output_data_dir, "genotype.tabular", genotype_table_tibble);

# Output the file needed for populating the person table.
person_table_data_frame <- data.frame(matrix(ncol=4, nrow=num_rows));
colnames(person_table_data_frame) <- c("last_name", "first_name", "organization", "email");