SB Taxonomic breakdown

--taxonomic_breakdown, -tb

Implemented in version 1.3

Description

If records are annotated with organism metadata, such as you would find in RefSeq records downloaded from GenBank in GenBank format, this function will give an organized breakdown of the taxonomic spread of those records.

Argument

Depth ( int )

Optional. Specify how deeply to step into the taxonomy. The default value is 5, and to go all the way to the species level of all records, pass in the value 0.

Examples

Input file: caspase.gb

LOCUS       XP_010711755             100 aa            linear   VRT 20-DEC-2016
DEFINITION  PREDICTED: caspase-8 [Meleagris gallopavo].
ACCESSION   XP_010711755
VERSION     XP_010711755.1
KEYWORDS    .
SOURCE      Meleagris gallopavo (turkey)
  ORGANISM  Meleagris gallopavo
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
            Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
            Phasianidae; Meleagridinae; Meleagris.
FEATURES             Location/Qualifiers
ORIGIN
        1 mssdfrkllf disealatee laalkflsle hvpvrkqedt eepkaffevl kekgmievgd
       61 lfflkellyr inridllash lgssreemer elqvpgkakv
//
LOCUS       XP_017108984             100 aa            linear   INV 16-JUN-2016
DEFINITION  PREDICTED: caspase Dronc [Drosophila bipectinata].
ACCESSION   XP_017108984
VERSION     XP_017108984.1
KEYWORDS    .
SOURCE      Drosophila bipectinata
  ORGANISM  Drosophila bipectinata
            Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
            Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
            Ephydroidea; Drosophilidae; Drosophila; Sophophora.
FEATURES             Location/Qualifiers
ORIGIN
        1 mqppnkeigm lekhrkhism nldklvratn ytkianecvr vgiissqmrg fiedvkerfn
       61 mppeevlytq hcnlfekith rgpqaynqli qalrnvnyiq
//
LOCUS       XP_016915094             100 aa            linear   INV 09-JUN-2016
DEFINITION  PREDICTED: caspase-8 [Apis cerana].
ACCESSION   XP_016915094
VERSION     XP_016915094.1
KEYWORDS    .
SOURCE      Apis cerana (Asiatic honeybee)
  ORGANISM  Apis cerana
            Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
            Pterygota; Neoptera; Holometabola; Hymenoptera; Apocrita; Aculeata;
            Apoidea; Apidae; Apis.
FEATURES             Location/Qualifiers
ORIGIN
        1 mfsidalpnf avnnniskei lnkdilwkie ndfdidekis ilflmitdym hsfkiiydll
       61 kihqenktyi ltefinkypq nwknklleai ciiqnlqiir
//
LOCUS       XP_008512342             100 aa            linear   MAM 14-JUL-2014
DEFINITION  PREDICTED: caspase-14-like [Equus przewalskii].
ACCESSION   XP_008512342
VERSION     XP_008512342.1
KEYWORDS    .
SOURCE      Equus przewalskii (Przewalski's horse)
  ORGANISM  Equus przewalskii
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Laurasiatheria; Perissodactyla; Equidae; Equus.
FEATURES             Location/Qualifiers
ORIGIN
        1 mgggrrsgsd glrwpsktmp ameelqsrlq etldllspqe lrsfrrilkt vdeeprvlfl
       61 fyslfvkihp viprkvpkrs ydcvdgeldr ydlsgrrkaf
//
LOCUS       XP_013409672             100 aa            linear   INV 19-AUG-2015
DEFINITION  PREDICTED: caspase-8-like [Lingula anatina].
ACCESSION   XP_013409672
VERSION     XP_013409672.1
KEYWORDS    .
SOURCE      Lingula anatina
  ORGANISM  Lingula anatina
            Eukaryota; Metazoa; Lophotrochozoa; Brachiopoda; Linguliformea;
            Lingulata; Lingulida; Linguloidea; Lingulidae; Lingula.
FEATURES             Location/Qualifiers
ORIGIN
        1 mstnreekvk vwpctvelfe kkaydakrvy knytewrgra viinnvsfdn efsldrkgte
       61 vdveylkslf rqlhylvlkh dnltaeaidq latreartdh
//

Usage example 1

$: sb caspase.gb -tb

Output

Total: 5

Eukaryota    5
 |Metazoa    5
 | |Chordata    2
 | | |Craniata    2
 | | | |Vertebrata    2
 | |Ecdysozoa    2
 | | |Arthropoda    2
 | | | |Hexapoda    2
 | |Lophotrochozoa    1
 | | |Brachiopoda    1
 | | | |Linguliformea    1

Usage example 2

Specify a depth with an integer

$: sb caspase.gb -tb 3

Output

Total: 5

Eukaryota    5
 |Metazoa    5
 | |Chordata    2
 | |Ecdysozoa    2
 | |Lophotrochozoa    1

Usage example 3

Go all the way to the species level of every record by passing in the value 0

$: sb caspase.gb -tb 0

Output

Total: 5

Eukaryota    5
 |Metazoa    5
 | |Chordata    2
 | | |Craniata    2
 | | | |Vertebrata    2
 | | | | |Euteleostomi    2
 | | | | | |Archelosauria    1
 | | | | | | |Archosauria    1
 | | | | | | | |Dinosauria    1
 | | | | | | | | |Saurischia    1
 | | | | | | | | | |Theropoda    1
 | | | | | | | | | | |Coelurosauria    1
 | | | | | | | | | | | |Aves    1
 | | | | | | | | | | | | |Neognathae    1
 | | | | | | | | | | | | | |Galloanserae    1
 | | | | | | | | | | | | | | |Galliformes    1
 | | | | | | | | | | | | | | | |Phasianidae    1
 | | | | | | | | | | | | | | | | |Meleagridinae    1
 | | | | | | | | | | | | | | | | | |Meleagris    1
 | | | | | | | | | | | | | | | | | | |gallopavo    1
 | | | | | |Mammalia    1
 | | | | | | |Eutheria    1
 | | | | | | | |Laurasiatheria    1
 | | | | | | | | |Perissodactyla    1
 | | | | | | | | | |Equidae    1
 | | | | | | | | | | |Equus    1
 | | | | | | | | | | | |przewalskii    1
 | |Ecdysozoa    2
 | | |Arthropoda    2
 | | | |Hexapoda    2
 | | | | |Insecta    2
 | | | | | |Pterygota    2
 | | | | | | |Neoptera    2
 | | | | | | | |Holometabola    2
 | | | | | | | | |Diptera    1
 | | | | | | | | | |Brachycera    1
 | | | | | | | | | | |Muscomorpha    1
 | | | | | | | | | | | |Ephydroidea    1
 | | | | | | | | | | | | |Drosophilidae    1
 | | | | | | | | | | | | | |Drosophila    1
 | | | | | | | | | | | | | | |Sophophora    1
 | | | | | | | | | | | | | | | |bipectinata    1
 | | | | | | | | |Hymenoptera    1
 | | | | | | | | | |Apocrita    1
 | | | | | | | | | | |Aculeata    1
 | | | | | | | | | | | |Apoidea    1
 | | | | | | | | | | | | |Apidae    1
 | | | | | | | | | | | | | |Apis    1
 | | | | | | | | | | | | | | |cerana    1
 | |Lophotrochozoa    1
 | | |Brachiopoda    1
 | | | |Linguliformea    1
 | | | | |Lingulata    1
 | | | | | |Lingulida    1
 | | | | | | |Linguloidea    1
 | | | | | | | |Lingulidae    1
 | | | | | | | | |Lingula    1
 | | | | | | | | | |anatina    1