#!/usr/bin/env perl
use Test::Most;
use autodie;
use feature qw(say);
use Bio::MUST::Core;
my $class = 'Bio::MUST::Core::SeqId';
my @valid_ids = (
[ ('Arabidopsis halleri_81970@78182999') x 2, 0, 0, 0, 0, undef, undef,
'Arabidopsis', 'halleri', undef, '78182999', undef,
'81970', undef, undef, undef, undef, undef,
'78182999', undef, undef, undef,
'Arabidopsis halleri', 'A. halleri', 'Arabidopsis halleri_81970',
'Arabidopsis halleri 81970',
'Arabidopsis halleri 81970',
'Arabidopsis_halleri_81970@78182999',
q{'Arabidopsis halleri_81970@78182999'} ],
[ ('Micromonas sp._296587@255079694') x 2, 0, 0, '1', 0, undef, undef,
'Micromonas', 'sp.', undef, '255079694', undef,
'296587', undef, undef, undef, undef, undef,
'255079694', undef, undef, undef,
'Micromonas sp.', 'M. sp.', 'Micromonas sp._296587',
'Micromonas sp. 296587',
'Micromonas sp. 296587',
'Micromonas_sp._296587@255079694',
q{'Micromonas sp._296587@255079694'} ],
[ ('cp-Arabidopsis halleri_81970@78182999') x 2, 0, 0, 0, 0, 'cp', undef,
'Arabidopsis', 'halleri', undef, '78182999', undef,
'81970', undef, undef, undef, undef, undef,
'78182999', undef, undef, undef,
'Arabidopsis halleri', 'A. halleri', 'Arabidopsis halleri_81970',
'Arabidopsis halleri 81970',
'cp-Arabidopsis halleri 81970',
'cp-Arabidopsis_halleri_81970@78182999',
q{'cp-Arabidopsis halleri_81970@78182999'} ],
[ ('su3-Micromonas sp._296587@255079694') x 2, 0, 0, '1', 0, 'su3', undef,
'Micromonas', 'sp.', undef, '255079694', undef,
'296587', undef, undef, undef, undef, undef,
'255079694', undef, undef, undef,
'Micromonas sp.', 'M. sp.', 'Micromonas sp._296587',
'Micromonas sp. 296587',
'su3-Micromonas sp. 296587',
'su3-Micromonas_sp._296587@255079694',
q{'su3-Micromonas sp._296587@255079694'} ],
[ ('Capsella bursa-pastoris_3719@58003767') x 2, 0, 0, 0, 0, undef, undef,
'Capsella', 'bursa-pastoris', undef, '58003767', undef,
'3719', undef, undef, undef, undef, undef,
'58003767', undef, undef, undef,
'Capsella bursa-pastoris', 'C. bursa-pastoris', 'Capsella bursa-pastoris_3719',
'Capsella bursa-pastoris 3719',
'Capsella bursa-pastoris 3719',
'Capsella_bursa-pastoris_3719@58003767',
q{'Capsella bursa-pastoris_3719@58003767'} ],
[ ('cp-Capsella bursa-pastoris_3719@158513961') x 2, 0, 0, 0, 0, 'cp', undef,
'Capsella', 'bursa-pastoris', undef, '158513961', undef,
'3719', undef, undef, undef, undef, undef,
'158513961', undef, undef, undef,
'Capsella bursa-pastoris', 'C. bursa-pastoris', 'Capsella bursa-pastoris_3719',
'Capsella bursa-pastoris 3719',
'cp-Capsella bursa-pastoris 3719',
'cp-Capsella_bursa-pastoris_3719@158513961',
q{'cp-Capsella bursa-pastoris_3719@158513961'} ],
[ ('Pseudo-nitzschia multiseries_37319@194836') x 2, 0, 0, 0, 0, undef, undef,
'Pseudo-nitzschia', 'multiseries', undef, '194836', undef,
'37319', undef, undef, undef, undef, undef,
'194836', undef, undef, undef,
'Pseudo-nitzschia multiseries', 'P. multiseries', 'Pseudo-nitzschia multiseries_37319',
'Pseudo-nitzschia multiseries 37319',
'Pseudo-nitzschia multiseries 37319',
'Pseudo-nitzschia_multiseries_37319@194836',
q{'Pseudo-nitzschia multiseries_37319@194836'} ],
[ ('cp-Pseudo-nitzschia mannii_587315@111559260') x 2, 0, 0, 0, 0, 'cp', undef,
'Pseudo-nitzschia', 'mannii', undef, '111559260', undef,
'587315', undef, undef, undef, undef, undef,
'111559260', undef, undef, undef,
'Pseudo-nitzschia mannii', 'P. mannii', 'Pseudo-nitzschia mannii_587315',
'Pseudo-nitzschia mannii 587315',
'cp-Pseudo-nitzschia mannii 587315',
'cp-Pseudo-nitzschia_mannii_587315@111559260',
q{'cp-Pseudo-nitzschia mannii_587315@111559260'} ],
[ ('cp-d#Pseudo-nitzschia mannii_587315@111559260') x 2, 0, 0, 0, '1', 'cp', 'd',
'Pseudo-nitzschia', 'mannii', undef, '111559260', undef,
'587315', undef, undef, undef, undef, undef,
'111559260', undef, undef, undef,
'Pseudo-nitzschia mannii', 'P. mannii', 'Pseudo-nitzschia mannii_587315',
'Pseudo-nitzschia mannii 587315',
'cp-Pseudo-nitzschia mannii 587315',
'cp-d#Pseudo-nitzschia_mannii_587315@111559260',
q{'cp-d#Pseudo-nitzschia mannii_587315@111559260'} ],
[ ('nuppct#Vitrella brassicaformis_CCMP3155@ABC1234.1') x 2, 0, 0, 0, 0, undef, 'nuppct',
'Vitrella', 'brassicaformis', 'CCMP3155', 'ABC1234.1', undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Vitrella brassicaformis', 'V. brassicaformis', 'Vitrella brassicaformis_CCMP3155',
'Vitrella brassicaformis CCMP3155',
'Vitrella brassicaformis CCMP3155',
'nuppct#Vitrella_brassicaformis_CCMP3155@ABC1234.1',
q{'nuppct#Vitrella brassicaformis_CCMP3155@ABC1234.1'} ],
[ ('archaeon GW2011_AR10@CP010424') x 2, 0, 0, 0, 0, undef, undef,
'archaeon', 'GW2011_AR10', undef, 'CP010424', undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'archaeon GW2011_AR10', 'a. GW2011_AR10', 'archaeon GW2011_AR10',
'archaeon GW2011_AR10',
'archaeon GW2011_AR10',
'archaeon_GW2011_AR10@CP010424',
q{'archaeon GW2011_AR10@CP010424'} ],
[ ('Nessiteras rhombopteryx@PCR28S') x 2, 0, 0, 0, 0, undef, undef,
'Nessiteras', 'rhombopteryx', undef, 'PCR28S', undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Nessiteras rhombopteryx', 'N. rhombopteryx', 'Nessiteras rhombopteryx',
'Nessiteras rhombopteryx',
'Nessiteras rhombopteryx',
'Nessiteras_rhombopteryx@PCR28S',
q{'Nessiteras rhombopteryx@PCR28S'} ],
[ (q{Nessiteras rhombopteryx_'loch-ness'@PCR28S}) x 2, 0, 0, 0, 0, undef, undef,
'Nessiteras', 'rhombopteryx', q{'loch-ness'}, 'PCR28S', undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Nessiteras rhombopteryx', 'N. rhombopteryx', q{Nessiteras rhombopteryx_'loch-ness'},
q{Nessiteras rhombopteryx 'loch-ness'},
q{Nessiteras rhombopteryx 'loch-ness'},
q{Nessiteras_rhombopteryx_'loch-ness'@PCR28S},
q{'Nessiteras rhombopteryx_loch-ness@PCR28S'} ],
[ ('Arabidopsis halleri@ABB29495.1') x 2, 0, 0, 0, 0, undef, undef,
'Arabidopsis', 'halleri', undef, 'ABB29495.1', undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Arabidopsis halleri', 'A. halleri', 'Arabidopsis halleri',
'Arabidopsis halleri',
'Arabidopsis halleri',
'Arabidopsis_halleri@ABB29495.1',
q{'Arabidopsis halleri@ABB29495.1'} ],
[ ('Arabidopsis halleri_81970@ABB29495.1') x 2, 0, 0, 0, 0, undef, undef,
'Arabidopsis', 'halleri', undef, 'ABB29495.1', undef,
'81970', undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Arabidopsis halleri', 'A. halleri', 'Arabidopsis halleri_81970',
'Arabidopsis halleri 81970',
'Arabidopsis halleri 81970',
'Arabidopsis_halleri_81970@ABB29495.1',
q{'Arabidopsis halleri_81970@ABB29495.1'} ],
[ ('Arabidopsis halleri_halleri@78182999') x 2, 0, 0, 0, 0, undef, undef,
'Arabidopsis', 'halleri', 'halleri', '78182999', undef,
undef, undef, undef, undef, undef, undef,
'78182999', undef, undef, undef,
'Arabidopsis halleri', 'A. halleri', 'Arabidopsis halleri_halleri',
'Arabidopsis halleri halleri',
'Arabidopsis halleri halleri',
'Arabidopsis_halleri_halleri@78182999',
q{'Arabidopsis halleri_halleri@78182999'} ],
[ ('Arabidopsis halleri_halleri@ABB29495.1') x 2, 0, 0, 0, 0, undef, undef,
'Arabidopsis', 'halleri', 'halleri', 'ABB29495.1', undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Arabidopsis halleri', 'A. halleri', 'Arabidopsis halleri_halleri',
'Arabidopsis halleri halleri',
'Arabidopsis halleri halleri',
'Arabidopsis_halleri_halleri@ABB29495.1',
q{'Arabidopsis halleri_halleri@ABB29495.1'} ],
[ ('Nostoc azollae_0708@298493200') x 2, 0, 0, 0, 0, undef, undef,
'Nostoc', 'azollae', '0708', '298493200', undef,
undef, undef, undef, undef, undef, undef,
'298493200', undef, undef, undef,
'Nostoc azollae', 'N. azollae', 'Nostoc azollae_0708',
'Nostoc azollae 0708',
'Nostoc azollae 0708',
'Nostoc_azollae_0708@298493200',
q{'Nostoc azollae_0708@298493200'} ],
[ ('Anabaena sp._90@19612') x 2, 0, 0, '1', 0, undef, undef,
'Anabaena', 'sp.', undef, '19612', undef,
'90', undef, undef, undef, undef, undef,
'19612', undef, undef, undef,
'Anabaena sp.', 'A. sp.', 'Anabaena sp._90',
'Anabaena sp. 90',
'Anabaena sp. 90',
'Anabaena_sp._90@19612',
q{'Anabaena sp._90@19612'} ],
[ ('c#Oscarella sp._sn2011@OspS50623.H1.1...Parazoanthus_axinellae#NEW#') x 2, 0, '1', '1', '1', undef, 'c',
'Oscarella', 'sp.', 'sn2011', 'OspS50623.H1.1', 'Parazoanthus_axinellae',
undef, undef, undef, undef, undef, undef,
undef, undef, undef, 'Parazoanthus axinellae',
'Oscarella sp.', 'O. sp.', 'Oscarella sp._sn2011',
'Oscarella sp. sn2011',
'Oscarella sp. sn2011',
'c#Oscarella_sp._sn2011@OspS50623.H1.1...Parazoanthus_axinellae#NEW#',
q{'c#Oscarella sp._sn2011@OspS50623.H1.1...Parazoanthus_axinellae#NEW#'} ],
[ ('c#Oscarella carmela@Ocar68884.H1.1...Favella_ehrenbergii#NEW#') x 2, 0, '1', 0, '1', undef, 'c',
'Oscarella', 'carmela', undef, 'Ocar68884.H1.1', 'Favella_ehrenbergii',
undef, undef, undef, undef, undef, undef,
undef, undef, undef, 'Favella ehrenbergii',
'Oscarella carmela', 'O. carmela', 'Oscarella carmela',
'Oscarella carmela',
'Oscarella carmela',
'c#Oscarella_carmela@Ocar68884.H1.1...Favella_ehrenbergii#NEW#',
q{'c#Oscarella carmela@Ocar68884.H1.1...Favella_ehrenbergii#NEW#'} ],
[ ('Urticina eques@Uequ12160.E.lc#NEW#') x 2, 0, '1', 0, 0, undef, undef,
'Urticina', 'eques', undef, 'Uequ12160.E.lc', undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Urticina eques', 'U. eques', 'Urticina eques',
'Urticina eques',
'Urticina eques',
'Urticina_eques@Uequ12160.E.lc#NEW#',
q{'Urticina eques@Uequ12160.E.lc#NEW#'} ],
[ ('c#Pseudo-nitzschia australis_1024910ABMMETSP0142@CAMNT_0008229771.E.lc...Nostoc_azollae#NEW#') x 2, 0, '1', 0, '1', undef, 'c',
'Pseudo-nitzschia', 'australis', '1024910ABMMETSP0142', 'CAMNT_0008229771.E.lc', 'Nostoc_azollae',
undef, undef, undef, undef, undef, undef,
undef, undef, undef, 'Nostoc azollae',
'Pseudo-nitzschia australis', 'P. australis', 'Pseudo-nitzschia australis_1024910ABMMETSP0142',
'Pseudo-nitzschia australis 1024910ABMMETSP0142',
'Pseudo-nitzschia australis 1024910ABMMETSP0142',
'c#Pseudo-nitzschia_australis_1024910ABMMETSP0142@CAMNT_0008229771.E.lc...Nostoc_azollae#NEW#',
q{'c#Pseudo-nitzschia australis_1024910ABMMETSP0142@CAMNT_0008229771.E.lc...Nostoc_azollae#NEW#'} ],
[ ('Micromonas sp._296587@255079694') x 2, 0, 0, '1', 0, undef, undef,
'Micromonas', 'sp.', undef, '255079694', undef,
'296587', undef, undef, undef, undef, undef,
'255079694', undef, undef, undef,
'Micromonas sp.', 'M. sp.', 'Micromonas sp._296587',
'Micromonas sp. 296587',
'Micromonas sp. 296587',
'Micromonas_sp._296587@255079694',
q{'Micromonas sp._296587@255079694'} ],
[ ('Arabidopsis halleri_81970@ABB29495.1') x 2, 0, 0, 0, 0, undef, undef,
'Arabidopsis', 'halleri', undef, 'ABB29495.1', undef,
'81970', undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Arabidopsis halleri', 'A. halleri', 'Arabidopsis halleri_81970',
'Arabidopsis halleri 81970',
'Arabidopsis halleri 81970',
'Arabidopsis_halleri_81970@ABB29495.1',
q{'Arabidopsis halleri_81970@ABB29495.1'} ],
[ ('Listeria monocytogenes_GCA_000438585.1@AGR25087.1') x 2, 0, 0, 0, 0, undef, undef,
'Listeria', 'monocytogenes', undef, 'AGR25087.1', undef,
'GCA_000438585.1', 'GCA_000438585.1', 'GCA_000438585', '1', 'GCA', '000438585',
undef, undef, undef, undef,
'Listeria monocytogenes', 'L. monocytogenes', 'Listeria monocytogenes_GCA_000438585.1',
'Listeria monocytogenes GCA_000438585.1',
'Listeria monocytogenes GCA_000438585.1',
'Listeria_monocytogenes_GCA_000438585.1@AGR25087.1',
q{'Listeria monocytogenes_GCA_000438585.1@AGR25087.1'} ],
[ ('Listeria monocytogenes_GCF_000438585.1@AGR25087.1') x 2, 0, 0, 0, 0, undef, undef,
'Listeria', 'monocytogenes', undef, 'AGR25087.1', undef,
'GCF_000438585.1', 'GCF_000438585.1', 'GCF_000438585', '1', 'GCF', '000438585',
undef, undef, undef, undef,
'Listeria monocytogenes', 'L. monocytogenes', 'Listeria monocytogenes_GCF_000438585.1',
'Listeria monocytogenes GCF_000438585.1',
'Listeria monocytogenes GCF_000438585.1',
'Listeria_monocytogenes_GCF_000438585.1@AGR25087.1',
q{'Listeria monocytogenes_GCF_000438585.1@AGR25087.1'} ],
[ ('81970|ABB29495.1') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, 'ABB29495.1', undef,
'81970', undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'81970|ABB29495.1',
q{'81970|ABB29495.1'} ],
[ ('45351|NEMVEDRAFT_v1g121533-PA') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, 'NEMVEDRAFT_v1g121533-PA', undef,
'45351', undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'45351|NEMVEDRAFT_v1g121533-PA',
q{'45351|NEMVEDRAFT_v1g121533-PA'} ],
[ ('GCF_000438585.1|AGR25087.1') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, 'AGR25087.1', undef,
'GCF_000438585.1', 'GCF_000438585.1', 'GCF_000438585', '1', 'GCF', '000438585',
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'GCF_000438585.1|AGR25087.1',
q{'GCF_000438585.1|AGR25087.1'} ],
[ ('gi|404160475') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
'404160475', undef, undef, undef,
undef, undef, undef,
undef,
undef,
'gi|404160475',
q{'gi|404160475'} ],
[ ('gi|404160475|gb|AFR53081.1|') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, 'AFR53081.1', undef,
undef, undef, undef, undef, undef, undef,
'404160475', undef, undef, undef,
undef, undef, undef,
undef,
undef,
'gi|404160475|gb|AFR53081.1|',
q{'gi|404160475|gb|AFR53081.1|'} ],
[ ('gi|404160475|gb|AFR53081.1| AOX [Anthurium andraeanum]') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, 'AFR53081.1', undef,
undef, undef, undef, undef, undef, undef,
'404160475', undef, undef, undef,
undef, undef, undef,
undef,
undef,
'gi|404160475|gb|AFR53081.1| AOX [Anthurium andraeanum]',
q{'gi|404160475|gb|AFR53081.1| AOX [Anthurium andraeanum]'} ],
[ ('gi|11245480|gb|AAG33633.1|AF314254_1') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, 'AAG33633.1', undef,
undef, undef, undef, undef, undef, undef,
'11245480', undef, undef, undef,
undef, undef, undef,
undef,
undef,
'gi|11245480|gb|AAG33633.1|AF314254_1',
q{'gi|11245480|gb|AAG33633.1|AF314254_1'} ],
[ ('gi|11245480|gb|AAG33633.1|AF314254_1 alternative oxidase 1 [Chlamydomonas reinhardtii]') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, 'AAG33633.1', undef,
undef, undef, undef, undef, undef, undef,
'11245480', undef, undef, undef,
undef, undef, undef,
undef,
undef,
'gi|11245480|gb|AAG33633.1|AF314254_1 alternative oxidase 1 [Chlamydomonas reinhardtii]',
q{'gi|11245480|gb|AAG33633.1|AF314254_1 alternative oxidase 1 [Chlamydomonas reinhardtii]'} ],
[ ('gnl|EF-Ts_27|PF3D7_0305000') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, 'EF-Ts_27', 'PF3D7_0305000', undef,
undef, undef, undef,
undef,
undef,
'gnl|EF-Ts_27|PF3D7_0305000',
q{'gnl|EF-Ts_27|PF3D7_0305000'},
'gnl', 'EF-Ts_27', 'PF3D7_0305000' ],
[ ('gnl|met-10+|PF3D7_0914300') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, 'met-10+', 'PF3D7_0914300', undef,
undef, undef, undef,
undef,
undef,
'gnl|met-10+|PF3D7_0914300',
q{'gnl|met-10+|PF3D7_0914300'},
'gnl', 'met-10+', 'PF3D7_0914300' ],
[ ('gnl|TPx(Gl)_120|PF3D7_1212000') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, 'TPx(Gl)_120', 'PF3D7_1212000', undef,
undef, undef, undef,
undef,
undef,
'gnl|TPx(Gl)_120|PF3D7_1212000',
q{'gnl|TPx(Gl)_120|PF3D7_1212000'},
'gnl', 'TPx(Gl)_120', 'PF3D7_1212000' ],
[ ('gnl|OTUlcp2|PF3D7_1031400.2|more-stuff preserved description') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, 'OTUlcp2', 'PF3D7_1031400.2', undef,
undef, undef, undef,
undef,
undef,
'gnl|OTUlcp2|PF3D7_1031400.2|more-stuff preserved description',
q{'gnl|OTUlcp2|PF3D7_1031400.2|more-stuff preserved description'},
'gnl', 'OTUlcp2', 'PF3D7_1031400.2', 'more-stuff' ],
[ ('seq1') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'seq1',
q{'seq1'} ],
[ (q{Arthrospira platensis UTEX 'LB 2340' [88792662]}) x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
q{Arthrospira platensis UTEX 'LB 2340' [88792662]},
q{'Arthrospira platensis UTEX LB 2340 [88792662]'} ],
[ ('candidatus_methylomirabilis_oxyfera~GCA_000091165.1@FP565575~[[462948..463340]]=Bacteria-Candidate_division_nc10-unknown_class-unknown_order-unknown_family-Candidatus_methylomirabilis-Candidatus_methylomirabilis_oxyfera') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'candidatus_methylomirabilis_oxyfera~GCA_000091165.1@FP565575~[[462948..463340]]=Bacteria-Candidate_division_nc10-unknown_class-unknown_order-unknown_family-Candidatus_methylomirabilis-Candidatus_methylomirabilis_oxyfera',
q{'candidatus_methylomirabilis_oxyfera~GCA_000091165.1@FP565575~[[462948..463340]]=Bacteria-Candidate_division_nc10-unknown_class-unknown_order-unknown_family-Candidatus_methylomirabilis-Candidatus_methylomirabilis_oxyfera'} ],
[ ('candidatus_kinetoplastibacterium_crithidii|TCC036E~GCA_000340825.1@CP003804~[[809869..810243]]C=Bacteria-Proteobacteria-Betaproteobacteria-unknown_order-unknown_family-Kinetoplastibacterium-Candidatus_kinetoplastibacterium_crithidii') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'candidatus_kinetoplastibacterium_crithidii|TCC036E~GCA_000340825.1@CP003804~[[809869..810243]]C=Bacteria-Proteobacteria-Betaproteobacteria-unknown_order-unknown_family-Kinetoplastibacterium-Candidatus_kinetoplastibacterium_crithidii',
q{'candidatus_kinetoplastibacterium_crithidii|TCC036E~GCA_000340825.1@CP003804~[[809869..810243]]C=Bacteria-Proteobacteria-Betaproteobacteria-unknown_order-unknown_family-Kinetoplastibacterium-Candidatus_kinetoplastibacterium_crithidii'} ],
[ ('Escherichia_coli|ER2796~GCA_000800215.1@CP009644~[[4152126..4152491]]=Bacteria-Proteobacteria-Gammaproteobacteria-Enterobacteriales-Enterobacteriaceae-Escherichia-Escherichia_coli') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'Escherichia_coli|ER2796~GCA_000800215.1@CP009644~[[4152126..4152491]]=Bacteria-Proteobacteria-Gammaproteobacteria-Enterobacteriales-Enterobacteriaceae-Escherichia-Escherichia_coli',
q{'Escherichia_coli|ER2796~GCA_000800215.1@CP009644~[[4152126..4152491]]=Bacteria-Proteobacteria-Gammaproteobacteria-Enterobacteriales-Enterobacteriaceae-Escherichia-Escherichia_coli'} ],
[ ('Salmonella_enterica_subsp._enterica|SEROVARENTERITIDISEC20110358~GCA_000623335.1@CP007260~[[4225927..4226292]]=Bacteria-Proteobacteria-Gammaproteobacteria-Enterobacteriales-Enterobacteriaceae-Salmonella-Salmonella_enterica-Salmonella_enterica_subsp._enterica') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'Salmonella_enterica_subsp._enterica|SEROVARENTERITIDISEC20110358~GCA_000623335.1@CP007260~[[4225927..4226292]]=Bacteria-Proteobacteria-Gammaproteobacteria-Enterobacteriales-Enterobacteriaceae-Salmonella-Salmonella_enterica-Salmonella_enterica_subsp._enterica',
q{'Salmonella_enterica_subsp._enterica|SEROVARENTERITIDISEC20110358~GCA_000623335.1@CP007260~[[4225927..4226292]]=Bacteria-Proteobacteria-Gammaproteobacteria-Enterobacteriales-Enterobacteriaceae-Salmonella-Salmonella_enterica-Salmonella_enterica_subsp._enterica'} ],
[ ('Mycobacterium_tuberculosis|BEIJING/NITR203~GCA_000364825.1@CP005082~[[748789..749181]]=Bacteria-Actinobacteria-Actinobacteria-Corynebacteriales-Mycobacteriaceae-Mycobacterium-Mycobacterium_tuberculosis') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'Mycobacterium_tuberculosis|BEIJING/NITR203~GCA_000364825.1@CP005082~[[748789..749181]]=Bacteria-Actinobacteria-Actinobacteria-Corynebacteriales-Mycobacteriaceae-Mycobacterium-Mycobacterium_tuberculosis',
q{'Mycobacterium_tuberculosis|BEIJING/NITR203~GCA_000364825.1@CP005082~[[748789..749181]]=Bacteria-Actinobacteria-Actinobacteria-Corynebacteriales-Mycobacteriaceae-Mycobacterium-Mycobacterium_tuberculosis'} ],
[ ('Pycnococcus provasolii_41880@PROTID001') x 2, 0, 0, 0, 0, undef, undef,
'Pycnococcus', 'provasolii', undef, 'PROTID001', undef,
'41880', undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Pycnococcus provasolii', 'P. provasolii', 'Pycnococcus provasolii_41880',
'Pycnococcus provasolii 41880',
'Pycnococcus provasolii 41880',
'Pycnococcus_provasolii_41880@PROTID001',
q{'Pycnococcus provasolii_41880@PROTID001'} ],
[ ('Pycnococcus provasolii_RCC251_MMETSP1472_41880@PROTID001') x 2, 0, 0, 0, 0, undef, undef,
'Pycnococcus', 'provasolii', 'RCC251_MMETSP1472', 'PROTID001', undef,
'41880', undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Pycnococcus provasolii', 'P. provasolii', 'Pycnococcus provasolii_RCC251_MMETSP1472_41880',
'Pycnococcus provasolii RCC251_MMETSP1472 41880',
'Pycnococcus provasolii RCC251_MMETSP1472 41880',
'Pycnococcus_provasolii_RCC251_MMETSP1472_41880@PROTID001',
q{'Pycnococcus provasolii_RCC251_MMETSP1472_41880@PROTID001'} ],
[ ('Moorea producens_GCF_001854205.1@PROTID001') x 2, 0, 0, 0, 0, undef, undef,
'Moorea', 'producens', undef, 'PROTID001', undef,
'GCF_001854205.1', 'GCF_001854205.1', 'GCF_001854205', '1', 'GCF', '001854205',
undef, undef, undef, undef,
'Moorea producens', 'M. producens', 'Moorea producens_GCF_001854205.1',
'Moorea producens GCF_001854205.1',
'Moorea producens GCF_001854205.1',
'Moorea_producens_GCF_001854205.1@PROTID001',
q{'Moorea producens_GCF_001854205.1@PROTID001'} ],
[ ('Moorea producens_JHB_GCF_001854205.1@PROTID001') x 2, 0, 0, 0, 0, undef, undef,
'Moorea', 'producens', 'JHB', 'PROTID001', undef,
'GCF_001854205.1', 'GCF_001854205.1', 'GCF_001854205', '1', 'GCF', '001854205',
undef, undef, undef, undef,
'Moorea producens', 'M. producens', 'Moorea producens_JHB_GCF_001854205.1',
'Moorea producens JHB GCF_001854205.1',
'Moorea producens JHB GCF_001854205.1',
'Moorea_producens_JHB_GCF_001854205.1@PROTID001',
q{'Moorea producens_JHB_GCF_001854205.1@PROTID001'} ],
[ ('u#Emiliania huxleyi_PLYM219@CAMNT_0030889445') x 2, 0, 0, 0, '1', undef, 'u',
'Emiliania', 'huxleyi', 'PLYM219', 'CAMNT_0030889445', undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
'Emiliania huxleyi', 'E. huxleyi', 'Emiliania huxleyi_PLYM219',
'Emiliania huxleyi PLYM219',
'Emiliania huxleyi PLYM219',
'u#Emiliania_huxleyi_PLYM219@CAMNT_0030889445',
q{'u#Emiliania huxleyi_PLYM219@CAMNT_0030889445'} ],
# space-trailing ids (unparsable)
[ ('Arabidopsis halleri_81970@78182999 ') x 2, '1', undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef, undef,
undef, undef, undef, undef,
undef, undef, undef,
undef,
undef,
'Arabidopsis halleri_81970@78182999 ',
q{'Arabidopsis halleri_81970@78182999 '} ],
# quoted ids (from trees)
[ q{'Nematostella_vectensis_45351@NEMVEDRAFT_v1g166011-PA'}, 'Nematostella vectensis_45351@NEMVEDRAFT_v1g166011-PA', 0, 0, 0, 0, undef, undef,
'Nematostella', 'vectensis', undef, 'NEMVEDRAFT_v1g166011-PA', undef, '45351',
undef, undef, undef, undef, undef, undef, undef, undef, undef,
'Nematostella vectensis', 'N. vectensis', 'Nematostella vectensis_45351',
'Nematostella vectensis 45351', 'Nematostella vectensis 45351',
'Nematostella_vectensis_45351@NEMVEDRAFT_v1g166011-PA',
q{'Nematostella vectensis_45351@NEMVEDRAFT_v1g166011-PA'} ],
);
for my $exp_row (@valid_ids) {
my $seq_id = $class->new( full_id => $exp_row->[0] );
explain $seq_id->full_id;
my $got_row = [
$seq_id->full_id, # 0
$seq_id->is_foreign, # 1
$seq_id->is_new, # 2
$seq_id->is_genus_only, # 3
$seq_id->is_doubtful, # 4
$seq_id->family, # 5
$seq_id->tag, # 6
$seq_id->genus, # 7
$seq_id->species, # 8
$seq_id->strain, # 9
$seq_id->accession, # 10
$seq_id->tail, # 11
$seq_id->taxon_id, # 12
$seq_id->gca, # 13
$seq_id->gca_novers, # 14
$seq_id->gca_vers, # 15
$seq_id->gca_prefix, # 16
$seq_id->gca_number, # 17
$seq_id->gi, # 18
$seq_id->database, # 19
$seq_id->identifier, # 20
$seq_id->contam_org, # 21
$seq_id->org, # 22
$seq_id->abbr_org, # 23
$seq_id->full_org, # 24
$seq_id->full_org( q{ } ), # 25
$seq_id->family_then_full_org( q{ } ), # 26
$seq_id->foreign_id, # 27
$seq_id->nexus_id, # 28
$seq_id->all_parts, # 29 must be the last element because when undef
# it returns an empty list that flatens to no
# element and shortens the list by one and thus
# modifies array index
];
# explain $got_row;
is_deeply $got_row, [ @{$exp_row}[1..$#{$exp_row}] ],
"Built and queried SeqId: $exp_row->[0]";
}
my @ids2build = (
[ 'Arabidopsis halleri', '81970', '78182999',
'Arabidopsis halleri_81970@78182999' ],
[ 'Micromonas sp. RCC299', '296587', '255079694',
'Micromonas sp._296587@255079694' ],
[ 'Capsella bursa-pastoris', '3719', '158513961',
'Capsella bursa-pastoris_3719@158513961' ],
[ 'Pseudo-nitzschia multiseries', '37319', '194836',
'Pseudo-nitzschia multiseries_37319@194836' ],
[ 'Capsella bursa-pastoris', '3719', q{},
'Capsella bursa-pastoris_3719' ],
[ 'Ostreococcus \'lucimarinus\'', '242159', q{},
'Ostreococcus lucimarinus_242159' ],
[ 'Micromonas sp. RCC299', '296587', q{},
'Micromonas sp._296587' ],
[ 'Candidatus Phytoplasma mali', '37692', q{},
'Phytoplasma mali_37692' ],
[ 'Candidatus Arthromitus sp. SFB-rat-Yit', '1041504', q{},
'Arthromitus sp._1041504' ],
[ 'Candidatus Cloacamonas acidaminovorans str. Evry', '459349', q{},
'Cloacamonas acidaminovorans_459349' ],
[ 'Clostridium sticklandii', '1511', q{},
'Clostridium sticklandii_1511' ],
[ 'Clostridium sticklandii', q{}, q{},
'Clostridium sticklandii' ],
# TODO: add more ids! (test no species at all genus-like, viruses etc)
);
my @strains2build = (
[ 'Arabidopsis halleri', '81970', '78182999', 1,
'Arabidopsis halleri_81970@78182999' ],
[ 'Micromonas sp. RCC299', '296587', '255079694', 1,
'Micromonas sp._RCC299_296587@255079694' ],
[ 'Capsella bursa-pastoris', '3719', '158513961', 1,
'Capsella bursa-pastoris_3719@158513961' ],
[ 'Pseudo-nitzschia multiseries', '37319', '194836', 1,
'Pseudo-nitzschia multiseries_37319@194836' ],
[ 'Capsella bursa-pastoris', '3719', q{}, 1,
'Capsella bursa-pastoris_3719' ],
[ 'Ostreococcus \'lucimarinus\'', '242159', q{}, 1,
'Ostreococcus lucimarinus_242159' ],
[ 'Micromonas sp. RCC299', '296587', q{}, 1,
'Micromonas sp._RCC299_296587' ],
[ 'Candidatus Phytoplasma mali', '37692', q{}, 1,
'Phytoplasma mali_37692' ],
[ 'Candidatus Arthromitus sp. SFB-rat-Yit', '1041504', q{}, 1,
'Arthromitus sp._SFBratYit_1041504' ],
[ 'Candidatus Cloacamonas acidaminovorans str. Evry', '459349', q{}, 1,
'Cloacamonas acidaminovorans_Evry_459349' ],
[ 'Clostridium sticklandii', '1511', q{}, 1,
'Clostridium sticklandii_1511' ],
[ 'Clostridium sticklandii', q{}, q{}, 1,
'Clostridium sticklandii' ],
# TODO: add more ids! (test no species at all genus-like, viruses etc)
);
for my $exp_row (@ids2build) {
my $seq_id = $class->new_with(
org => $exp_row->[0],
taxon_id => $exp_row->[1],
accession => $exp_row->[2]
);
cmp_ok $seq_id->full_id, 'eq', $exp_row->[3],
"got expected SeqId: $exp_row->[3]";
}
for my $exp_row (@strains2build) {
my $seq_id = $class->new_with(
org => $exp_row->[0],
taxon_id => $exp_row->[1],
accession => $exp_row->[2],
keep_strain => $exp_row->[3]
);
cmp_ok $seq_id->full_id, 'eq', $exp_row->[4],
"got expected SeqId: $exp_row->[4]";
}
my @ids2clean = (
[ 'Candidatus Phytoplasma mali', 'Phytoplasma mali' ],
[ 'Candidatus Arthromitus sp. SFB-rat-Yit', 'Arthromitus sp. SFB-rat-Yit' ],
# TODO: check these
# [ 'uncultured cyanobacterium', 'cyanobacterium' ],
# [ 'uncultured actinobacterium WB039', 'actinobacterium WB039' ],
[ 'uncultured Candidatus Hamiltonella sp.', 'Hamiltonella sp.' ],
[ 'cf. Stagonospora sp. S619', 'Stagonospora sp. S619' ],
[ 'cf. Pavona sp. 2 DGL-2013', 'Pavona sp. 2 DGL-2013' ],
);
explain \@ids2clean;
for my $exp_row (@ids2clean) {
my $org = $class->clean_ncbi_name( $exp_row->[0] );
cmp_ok $org, 'eq', $exp_row->[1],
"got expected SeqId: $exp_row->[1]";
}
done_testing;