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Substitute scientific with common species names in a phylogenetic tree file

Step 1 - Generate a table with the scientific-common name correspondence

We need the correspondence between the scientific and common species names as described in the NCBI Taxonomy Database.

We want to do this for any number of species automatically, so we download the entire archive taxdump.tar.gz from the NCBI taxonomy database dump.

This archive contains the names.dmp file with the format:

10090	|	house mouse	|		|	genbank common name	|
10090	|	LK3 transgenic mice	|		|	includes	|
10090	|	mouse	|	mouse <Mus musculus>	|	common name	|
10090	|	Mus musculus Linnaeus, 1758	|		|	authority	|
10090	|	Mus musculus	|		|	scientific name	|
10090	|	Mus sp. 129SV	|		|	includes	|
10090	|	nude mice	|		|	includes	|
10090	|	transgenic mice	|		|	includes	|

Make new folder for this exercise and cd into it. Download the file and extract the names.dmp

$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
$ tar -xvf taxdump.tar.gz names.dmp

taxdump.tar.gz    51MB
names.dmp        189MB
  • We want to convert this table into a tab delimited file with this format:
​​   taxonID    scientific_name	    common_name    genbank_common_name
​​   10090      Mus musculus         mouse	    house mouse
  • We want to add an underscore between the genus (e.g. Mus) and the specific name of the species (e.g. musculus), so the scientific name is listed as in the tree file (e.g Mus_musculus).
  • We want to capitalize the first word in the common name (if not already capitalized).

Step 2 - Edit the phylogenetic tree file

The phylogenetic tree file used for the 100way alignment is hg38.100way.scientificNames.nh.
It can be downloaded from here and details could be found here.

Download the file (4.1KB).

wget http://hgdownload.cse.ucsc.edu/goldenpath/hg38/multiz100way/hg38.100way.scientificNames.nh

The format of the tree file is

	((((((((((((((((((Homo_sapiens:0.00655,
                 Pan_troglodytes:0.00684):0.00422,
                Gorilla_gorilla_gorilla:0.008964):0.009693,
               Pongo_pygmaeus_abelii:0.01894):0.003471,
              Nomascus_leucogenys:0.02227):0.01204,
             (((Macaca_mulatta:0.004991,
               Macaca_fascicularis:0.004991):0.003,
              Papio_anubis:0.008042):0.01061,
             Chlorocebus_sabaeus:0.027):0.025):0.02183,
            (Callithrix_jacchus:0.03,
            Saimiri_boliviensis:0.01035):0.01965):0.07261,
           Otolemur_garnettii:0.13992):0.013494,
          Tupaia_chinensis:0.174937):0.002,
         (((Spermophilus_tridecemlineatus:0.125468,

See a description of the Newick tree format here.

The phylogenetic tree could be visualized online at https://itol.embl.de/ (notice that this application takes care of removing the _ from the scientific name).

Before

After

Step 1

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The files are in Windows/DOS ASCII text, with CRLF line terminators format which makes awk to misbehave. Check your files and convert them to UNIX format if necessary.

# check the format
$ file filename
filename: ASCII text, with CRLF line terminators

# Convert to unix format
$ dos2unix filename
dos2unix: converting file filename to Unix format ...

# check again
$ file filename
filename: ASCII text

Let's first tabulate the NCBI Taxonomy Database in more convenient format for us - getting the relevant information on single line, replace some spaces with underscore symbol _, remove the extra blanks in fron and after the names, etc.

names.tab

9605|Homo|Humans|
9606|Homo_sapiens|Man|
9608|Canidae|Dog, coyote, wolf, fox|
9611|Canis||
9612|Canis_lupus|Grey wolf|
9614|Canis_latrans|Coyote|
9615|Canis_lupus_familiaris|Dogs|
9616|Canis_sp.||
9619|Dusicyon||
9620|Cerdocyon_thous|Crab-eating fox|
9621|Lycaon||
9622|Lycaon_pictus|Painted hunting dog|
9623|Otocyon||
9624|Otocyon_megalotis|Bat-eared fox|
9625|Vulpes||
9626|Vulpes_chama|Cape fox|
9627|Vulpes_vulpes|Silver fox|
9629|Vulpes_corsac|Corsac fox|
9630|Vulpes_macrotis|Kit fox|
9631|Vulpes_velox|Swift fox|

Might not be the best solution but it is easy to read and modify, for now. Note, we do not need to sort but it will look better if we have the final result in order.

$ ./01.tabulate-names.awk names.dmp | sort -g -k 1 > names.tab

Code will appear here after some discussions.
Just refresh the page when it is revealed.

01.tabulate-names.awk

#!/usr/bin/awk -f
BEGIN{
  FS="|"
#  print "#taxonID scientific_name        common_name     genbank_common_name"
}

$4 ~ "scientific name"     { sciname[$1*1]=  unds(Clean($2)); next}

$4 ~ "common name"         { com_name[$1*1]= Cap(Clean($2));  next}

$4 ~ "genbank common name" { genbank[$1*1]=  unds(Clean($2)); next}

END{
  for(i in sciname) print i"|"sciname[i]"|"com_name[i]"|"genbank[i]
}

# Function declarations ==============================

function Clean (string){
  sub(/^[ \t]+/, "",string)
  sub(/[ \t]+$/, "",string)
  return string
}

function unds(string) { gsub(" ","_",string); return string}

function Cap (string) { return toupper(substr(string,0,1))substr(string,2) }

Step 2

Now we can use the tabulated data in names.tab and perform the replacement in hg38.100way.scientificNames.nh by matching the scientific names in $2 with the common names in $3 - we use FS="|"

((((((((((((((((((Man:0.00655,
                 Chimpanzee:0.00684):0.00422,
                Western lowland gorilla:0.008964):0.009693,
               Pongo_pygmaeus_abelii:0.01894):0.003471,
              White-cheeked Gibbon:0.02227):0.01204,
             (((Rhesus monkeys:0.004991,
               Long-tailed macaque:0.004991):0.003,
              Olive baboon:0.008042):0.01061,
             Green monkey:0.027):0.025):0.02183,
            (White-tufted-ear marmoset:0.03,
            Bolivian squirrel monkey:0.01035):0.01965):0.07261,
           Small-eared galago:0.13992):0.013494,

Again, this might not be the best way but it works. The suggested solutions could be easily merged into a single script. I would prefer to have them in steps, so I can make sure that the first step has completed successfully (it takes some time) before I continue. Also I can filter the unnecessary data in the newly tabulated file and use only relevant data or alter further if I need.

$ ./02.substitute.awk names.tab hg38.100way.scientificNames.nh

Code will appear here after some discussions.
Just refresh the page when it is revealed.

#!/usr/bin/awk -f
BEGIN{
  FS="|"
#  print "#taxonID scientific_name        common_name     genbank_common_name"
}

NR== FNR{ map[$2]= $3; next}

{
  line= $0
  gsub("[0-9.,;:)( ]","")
  if ( $0 in map) sub($0,map[$0],line)
  print line
}


tags: awk bioawk UPPMAX SNIC
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