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ropensci / taxa

taxonomic classes for R
https://docs.ropensci.org/taxa
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Taxmap print method adds `NA` when character vector is of long strings #114

Closed zachary-foster closed 6 years ago

zachary-foster commented 6 years ago 
> silva
<Taxmap>
  8577 taxa: aab. Bacteria, aac. Eukaryota, aad. Archaea ... shz. MD-2014, sia. ssp. JD-2011, sib. R570
  8577 edges: NA->aab, NA->aac, NA->aad, aab->aae, aab->aaf ... sgy->shx, shf->shy, shi->shz, shm->sia, shw->sib
  3 data sets:
    tax_data:
      # A tibble: 10,000 x 4
        taxon_id ncbi_id  start_pos end_pos
        <chr>    <chr>    <chr>     <chr>  
      1 jmy      JF756592 1         1450   
      2 jmz      KM995838 1         1408   
      3 qsn      KP276470 1         1713   
      # ... with 9,997 more rows
    class_data:
      # A tibble: 77,516 x 4
        taxon_id input_index name       other_name
        <chr>          <int> <chr>      <chr>     
      1 aab                1 Bacteria   ""        
      2 aae                1 Firmicutes ""        
      3 acx                1 Bacilli    ""        
      # ... with 7.751e+04 more rows
    silva_seq:  GGUGCGGCGUCUAUACAUGCAGUCGAGCGAACAGAAAAGGAGCUUGCUCCUUUGACGUUAGCGGCGGACGGGUGAGUAACACGUGGGCAACCUACCCUAUAGUUUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGAAUAAUCUCUUUUACUUCAUGGUGAAAGACUGAAAGACGGUUUCGGCUGUCGCUAUAGGAUGGGCCCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGAUGCGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCACAAUGGGCGAAAGCCUGAUGGAGCAACGCCGCGUGAGUGAAGAAGGUUUUCGGAUCGUAAAACUCUGUUGUAAGGGAAGAACAAGUACAGUAGUAACUGGCUGUACCUUGACGGUACCUUAUUAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGCGCGCGCAGGCGGUCCUUUAAGUCUGAUGUGAAAGCCCACGGCUCAACCGUGGAGGGUCAUUGGAAACUGGGGGACUUGAGUGCAGAAGAGGAAAGUGGAAUUCCAAGUGUAGCGGUGAAAUGCGUAGAGAUUUGGAGGAACACCAGUGGCGAAGGCGACUUUCUGGUCUGUAACUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCCGUUGACCACUGUAGAGAUAUAGUUUCCCCUUCGGGGGCAACGGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCAUCAUUUAGUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACGAUACAAACGGUUGCCAACUCGCGAGAGGGAGCUAAUCCGAUAAAGUCGUUCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGUCGGUGAGGUAACCUUUUGGAGCCAGCCGCUCGAAGGUGCAUGG ... NA, CGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCGCUUCGGUGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAACACUCUGUCCCGCAUGGGACGGGGUUGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCUAGCUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUAUACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCCGCGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUNGAAGGUGGG
  0 functions:
> sum(silva$data$silva_seq == "NA")
[1] 0
> sum(is.na(silva$data$silva_seq))
[1] 0