Bio-MUST-Core
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lib/Bio/MUST/Core/SeqId.pm view on Meta::CPAN
RBG-16-64-13
RBG-16-64-22
RBG-16-64-32
RBG-16-64-43
RBG-16-65-34
RBG-16-66-20
RBG-16-66-30
RBG-16-68-12
RBG-16-68-14
RBG-16-68-21
RBG-16-71-46
RBS10-35
RDHV-like
Reagent-associated
Red-bellied
Red-billed
Red-capped
Red-crowned
Red-eared
Red-faced
Red-fronted
Red-handed
Red-necked
Red-recombineering
red-rumped
REDSEA-S09-B13
Regulator-reporter
Reoviridae-like
Reptile-associated
Retro-megavirus
Retropinna-associated
RH-AL1
RH-chloro-G1
RH2-MAG17b
Rhabdoviridae-like
RHBSTW-00994
Rhinopithecus-associated
RI-106
RI-112
RI-121
RI-153
RI-182
RI-185
RI-211
RI-212
RI-213
RI-231
RI-242
RI-283
RI-29
RI-34
RI-342
RI-382
RI-421
RI-43
RI-461
RI-55
RI-92
RI-95
rice-associated
Rigidomastix-like
RIOMV-3
RIOMV-4
Rm-Bat-CoV
RML-105355
rod-shaped
Rodent-like
root-associated
Rosaceae-associated
Roseobacter-like
Rous-associated
rpL23-fusion
Rs-D84
Rubrivivax-like
Rudolf-kamelinia
RumEn-M2
RV-African
RV-Bower
RV-Brook
RV-Brown
RV-Common
RV-Edible
RV-European
RV-Freshwater
RV-Gharial
RV-Horse
RV-Iberian
RV-Leopard
RV-Painted
RV-Palmate
RV-Pit
RV-Pufferfish
RV-Rhinatremid
RV-Rocket
RV-Slider
RV-Stickleback
RV-Stripe
RV-Tiger
RV-Tinamou
RV-Tuatara
RVA/Human-wt/MWI/1473/2001/G8P4
RVA/Human-wt/ZAF/3133WC/2009/G12P4
RVA/Human-wt/ZAF/3176WC/2009/G12P6
RVA/Human-wt/ZAF/3203WC/2009/G2P4
RVW-14
RYN-111
RYN-115
RYN-117
RYN-122
RYN-124
RYN-133
RYN-140
RYN-150
RYN-170
RYN-182
RYN-227
RYN-230
RYN-353
RYN-404
RYN-405
RYN-417
lib/Bio/MUST/Core/SeqId.pm view on Meta::CPAN
fluorescens_BZ
fluorescens_CB
fluorescens_CC
fluorescens_CD
fluorescens_CE
fluorescens_G
fluorescens_H
fluorescens_M
fluorescens_Q
fluorescens_S
fluorescens_W
fluorescens_X
fluvialis_A
fluvialis_B
fluvialis_C
fluvialis_D
fluvialis_E
fluvialis_F
fluviatilis_A
fluvii_A
FMAS_PN2
FMAS_PN3
FMAS_PN5
foliaceum_A
foliorum_B
fonticola_A
fonticola_B
fonticola_C
formicae_A
formicicum_A
formicilis_A
formicilis_B
formigenes_C
formigenes_D
formigenes_E
formosense_A
formosum_A
forsythia_A
fortis_A
FR1_11-MR-2014
FR1_16_MR-2014
FR3_2_MR-2014
fragariae_A
fragi_D
fragilis_A
fragilis_B
frankenforstense_A
franklandus_A
frederiksbergense_A
frederiksbergense_B
frederiksbergensis_A
frederiksbergensis_B
frederiksbergensis_D
frederiksbergensis_F
frederiksbergensis_G
frederiksbergensis_H
frederiksbergensis_I
fredii_A
fredii_B
fredii_C
frigidaeris_A
frigidisoli_A
frigiditerrae_A
frigidus_A
frigoris_A
frigoritolerans_A
frigoritolerans_B
frisingense_B
fugitiva_A
fulva_A
fulva_B
fulva_C
fulva_D
fulvum_A
fulvum_B
fungivorans_A
fungivorans_B
fungorum_A
fungorum_B
furvisabuli_A
fuscovaginae_A
fuscovaginae_B
fuscus_A
fusiformis_A
fusiformis_D
fusiformis_E
fusiformis_F
G01_1mb_b10_2005-12-15
G3_GreenLake
G5_GreenLake
G7_8_4BO2
G_01
G_02
G_05
G_10
G_14
G_20
G_22
G_23
gaetbuli_A
gaetbuli_B
galactitolivorans_A
galegae_A
galegae_B
galegae_C
galegae_D
gallaeciensis_A
gallinacea_A
gallolyticus_B
gallolyticus_C
gandavensis_A
gandavensis_B
gandavensis_C
gangwonense_A
garvieae_A
gastricus_A
gaviniae_A
gazogenes_A
gelatinosus_A
gelatinosus_B
geoffroys_cat/URU-01/2009
geofontis_A
georgiana_A
geothermicum_A
lib/Bio/MUST/Core/SeqId.pm view on Meta::CPAN
wratislaviensis_A
WS01_1416
WS01_480
WS06_481
WS08_522
WS10_380
WS12_472
WS13_484
WS18_483
WS19_479
wynnii_A
XAN_1
XAN_14
XAN_8
xanthomarina_A
xanthopallidus_B
xanthophaeus_A
xanthus_A
xanthus_B
xenophagum_A
xiamenensis_A
xiamenensis_B
xinganensis_A
xinjiangensis_A
xylanexedens_A
xylanexedens_B
xylanexedens_C
xylanilyticus_A
xylanilyticus_B
xylanivorans_A
xylanolytica_B
xylanophilus_A
xyli_A
xyli_C
xylinus_C
xylinus_D
xylinus_E
xylosoxidans_B
xylosoxidans_C
xylosoxidans_D
xylosus_B
XZ110_XZ_CHN_2017
XZ111_XZ_CHN_2017
XZ112_XZ_CHN_2017
XZ114_XZ_CHN_2017
XZ115_XZ_CHN_2017
XZ93_XZ_CHN_2017
XZ97_XZ_CHN_2017
XZ98_XZ_CHN_2017
XZ99_XZ_CHN_2017
Y2H-GFP_URA3
Y4_579_1
yabuuchiae_A
yamanorum_A
yanchengensis_A
yanglingense_A
yannicii_A
yanoikuyae_A
yanshanensis_A
yeojuensis_A
yomogidense_A
yonginensis_A
YS1-2_2434
YS1-2_2437
yuanmingense_A
zalophi_A
zeae_A
zhangzhouensis_A
zhoushanensis_A
zoogloeoides_A
zoogloeoides_B
zoogloeoides_C
zucineum_B
zundukense_A
zymae_A
);
my %is_hyphenated = map { $_ => 1 } @GENERA;
my %is_underscored = map { $_ => 1 } @SPECIES;
sub _set_gca_and_or_taxon_id {
my $self = shift;
my $strain = shift;
# Note: we use named captures here (?<capture name> ... )
## no critic (ProhibitUnusedCapture)
# handle GCA/GCF acting as taxon_ids
if ($strain =~ m/\A (:?(?<strain>.*)_)? (?<gca>$NCBIGCA) \z/xms) {
# truncate strain to optional non-GCA/GCF part (excl. underscore)...
# ... and set taxon_id to full GCA/GCF
$self->_set_strain($+{strain});
my $gca = $+{gca};
$self->_set_taxon_id($gca);
$self->_set_gca( $gca); # alias
# further store GCA/GCF components for easier comparison
my ($gca_novers, $gca_vers) = split /\./xms, $gca;
$self->_set_gca_novers($gca_novers);
$self->_set_gca_vers( $gca_vers );
my ($gca_prefix, $gca_number) = split /_/xms, $gca_novers;
$self->_set_gca_prefix($gca_prefix);
$self->_set_gca_number($gca_number);
}
# handle regular taxon_ids
elsif ($strain =~ m/\A (:?(?<strain>.*)_)? (?<taxon_id>$NCBIPKEY) \z/xms) {
# truncate strain to optional non-taxon_id part (excl. underscore)...
# ... and set taxon_id
$self->_set_strain( $+{strain });
$self->_set_taxon_id($+{taxon_id});
}
## use critic
# ignore legacy strains
return;
}
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