Update original csv #7
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looks like latest changes regarding formatting of pH_Optimum values are not yet merged |
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here is my suggestion for critical Species names:
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to allow copy and paste, same table as above
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Hallo Stefan, könntest du mir bitte sagen welche Tabelle bzw in welchem
Branch genau du als new und old bezeichnest?
…On Wed, 31 Aug 2022 at 09:07, Stefan Janssen ***@***.***> wrote:
to allow copy and paste, same table as above
<title></title>
<meta name="generator" content="LibreOffice 6.4.7.2 (Linux)"/>
<style type="text/css">
body,div,table,thead,tbody,tfoot,tr,th,td,p { font-family:"Liberation Sans"; font-size:x-small }
a.comment-indicator:hover + comment { background:#ffd; position:absolute; display:block; border:1px solid black; padding:0.5em; }
a.comment-indicator { background:red; display:inline-block; border:1px solid black; width:0.5em; height:0.5em; }
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</style>
old_Genus old_Species new_Genus new_Species 0 stefans suggestion
Anaerosalibacter Anaerosalibacter sp. Anaerosalibacter sp 1 Anaerosalibacter
sp.
Aphanizomenon flos-aquae Aphanizomenon aquae 7 flos-aquae
Bacillus Bacillus safensis subsp. osmophilus Bacillus safensis 7 safensis
Brevundimonas Brevundimonas sp. Brevundimonas sp 1 Brevundimonas sp.
Dolichospermum flos-aquae Dolichospermum aquae 7 flos-aquae
Finegoldia Finegoldia sp. Finegoldia sp 1 Finegoldia sp.
Halomonas denitri<81>cans Halomonas a5 8 denitrificans
Methanothermobacter Methanothermobacter sp. Methanothermobacter sp 2 Methanothermobacter
sp.
Mucilaginibacter rigui Mucilaginibacter rigui Mucilaginibacter rigui rigui
6 rigui
Mycobacterium gordonae Mycobacterium paragordonae Mycobacterium gordonae
paragordonae 3 paragordonae
Oscillatoria nigro-viridis Oscillatoria viridis 4 nigro-viridis
Paulownia witches-broom Paulownia broom 3 witches-broom
Plasticicumulans not yet known; article proposed:Plasticicumulans
lactativoran Plasticicumulans yet 5 lactativoran
Pseudoclavibacter Pseudoclavibacter sp. Pseudoclavibacter sp 14 Pseudoclavibacter
sp.
Ruania albidi<89>ava Ruania a5 8 albidiflava
Selenomonas Selenomonas sp. Selenomonas sp 1 Selenomonas sp.
Sphingobacterium Sphingobacterium composti [homonym] Sphingobacterium
composti 7 composti
Thalassospira A40-3 Thalassospira 3 1 A40-3
Thermovibrio ammoni<81>cans Thermovibrio a5 10 ammonificans
archaeon GW2011_AR10 archaeon AR10 3 GW2011_AR10
archaeon GW2011_AR20 archaeon AR20 3 GW2011_AR20
haloarchaeon 3A1-DGR haloarchaeon DGR 3 3A1-DGR
olei IMMIBHF-1T olei 1T 2 IMMIBHF-1T
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Old=Main, new= Dein PR #7
GuiraudTresor ***@***.***> schrieb am Do., 1. Sept. 2022,
12:51:
… Hallo Stefan, könntest du mir bitte sagen welche Tabelle bzw in welchem
Branch genau du als new und old bezeichnest?
On Wed, 31 Aug 2022 at 09:07, Stefan Janssen ***@***.***>
wrote:
> to allow copy and paste, same table as above
>
> <title></title>
>
> <meta name="generator" content="LibreOffice 6.4.7.2 (Linux)"/>
>
> <style type="text/css">
>
> body,div,table,thead,tbody,tfoot,tr,th,td,p { font-family:"Liberation
Sans"; font-size:x-small }
>
> a.comment-indicator:hover + comment { background:#ffd;
position:absolute; display:block; border:1px solid black; padding:0.5em; }
>
> a.comment-indicator { background:red; display:inline-block; border:1px
solid black; width:0.5em; height:0.5em; }
>
> comment { display:none; }
>
> </style>
>
>
> old_Genus old_Species new_Genus new_Species 0 stefans suggestion
> Anaerosalibacter Anaerosalibacter sp. Anaerosalibacter sp 1
Anaerosalibacter
> sp.
> Aphanizomenon flos-aquae Aphanizomenon aquae 7 flos-aquae
> Bacillus Bacillus safensis subsp. osmophilus Bacillus safensis 7
safensis
> Brevundimonas Brevundimonas sp. Brevundimonas sp 1 Brevundimonas sp.
> Dolichospermum flos-aquae Dolichospermum aquae 7 flos-aquae
> Finegoldia Finegoldia sp. Finegoldia sp 1 Finegoldia sp.
> Halomonas denitri<81>cans Halomonas a5 8 denitrificans
> Methanothermobacter Methanothermobacter sp. Methanothermobacter sp 2
Methanothermobacter
> sp.
> Mucilaginibacter rigui Mucilaginibacter rigui Mucilaginibacter rigui
rigui
> 6 rigui
> Mycobacterium gordonae Mycobacterium paragordonae Mycobacterium gordonae
> paragordonae 3 paragordonae
> Oscillatoria nigro-viridis Oscillatoria viridis 4 nigro-viridis
> Paulownia witches-broom Paulownia broom 3 witches-broom
> Plasticicumulans not yet known; article proposed:Plasticicumulans
> lactativoran Plasticicumulans yet 5 lactativoran
> Pseudoclavibacter Pseudoclavibacter sp. Pseudoclavibacter sp 14
Pseudoclavibacter
> sp.
> Ruania albidi<89>ava Ruania a5 8 albidiflava
> Selenomonas Selenomonas sp. Selenomonas sp 1 Selenomonas sp.
> Sphingobacterium Sphingobacterium composti [homonym] Sphingobacterium
> composti 7 composti
> Thalassospira A40-3 Thalassospira 3 1 A40-3
> Thermovibrio ammoni<81>cans Thermovibrio a5 10 ammonificans
> archaeon GW2011_AR10 archaeon AR10 3 GW2011_AR10
> archaeon GW2011_AR20 archaeon AR20 3 GW2011_AR20
> haloarchaeon 3A1-DGR haloarchaeon DGR 3 3A1-DGR
> olei IMMIBHF-1T olei 1T 2 IMMIBHF-1T
>
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alles klar. danke
On Thu, 1 Sept 2022 at 12:56, Stefan Janssen ***@***.***>
wrote:
… Old=Main, new= Dein PR #7
GuiraudTresor ***@***.***> schrieb am Do., 1. Sept. 2022,
12:51:
> Hallo Stefan, könntest du mir bitte sagen welche Tabelle bzw in welchem
> Branch genau du als new und old bezeichnest?
>
> On Wed, 31 Aug 2022 at 09:07, Stefan Janssen ***@***.***>
> wrote:
>
> > to allow copy and paste, same table as above
> >
> > <title></title>
> >
> > <meta name="generator" content="LibreOffice 6.4.7.2 (Linux)"/>
> >
> > <style type="text/css">
> >
> > body,div,table,thead,tbody,tfoot,tr,th,td,p { font-family:"Liberation
> Sans"; font-size:x-small }
> >
> > a.comment-indicator:hover + comment { background:#ffd;
> position:absolute; display:block; border:1px solid black; padding:0.5em;
}
> >
> > a.comment-indicator { background:red; display:inline-block; border:1px
> solid black; width:0.5em; height:0.5em; }
> >
> > comment { display:none; }
> >
> > </style>
> >
> >
> > old_Genus old_Species new_Genus new_Species 0 stefans suggestion
> > Anaerosalibacter Anaerosalibacter sp. Anaerosalibacter sp 1
> Anaerosalibacter
> > sp.
> > Aphanizomenon flos-aquae Aphanizomenon aquae 7 flos-aquae
> > Bacillus Bacillus safensis subsp. osmophilus Bacillus safensis 7
> safensis
> > Brevundimonas Brevundimonas sp. Brevundimonas sp 1 Brevundimonas sp.
> > Dolichospermum flos-aquae Dolichospermum aquae 7 flos-aquae
> > Finegoldia Finegoldia sp. Finegoldia sp 1 Finegoldia sp.
> > Halomonas denitri<81>cans Halomonas a5 8 denitrificans
> > Methanothermobacter Methanothermobacter sp. Methanothermobacter sp 2
> Methanothermobacter
> > sp.
> > Mucilaginibacter rigui Mucilaginibacter rigui Mucilaginibacter rigui
> rigui
> > 6 rigui
> > Mycobacterium gordonae Mycobacterium paragordonae Mycobacterium
gordonae
> > paragordonae 3 paragordonae
> > Oscillatoria nigro-viridis Oscillatoria viridis 4 nigro-viridis
> > Paulownia witches-broom Paulownia broom 3 witches-broom
> > Plasticicumulans not yet known; article proposed:Plasticicumulans
> > lactativoran Plasticicumulans yet 5 lactativoran
> > Pseudoclavibacter Pseudoclavibacter sp. Pseudoclavibacter sp 14
> Pseudoclavibacter
> > sp.
> > Ruania albidi<89>ava Ruania a5 8 albidiflava
> > Selenomonas Selenomonas sp. Selenomonas sp 1 Selenomonas sp.
> > Sphingobacterium Sphingobacterium composti [homonym] Sphingobacterium
> > composti 7 composti
> > Thalassospira A40-3 Thalassospira 3 1 A40-3
> > Thermovibrio ammoni<81>cans Thermovibrio a5 10 ammonificans
> > archaeon GW2011_AR10 archaeon AR10 3 GW2011_AR10
> > archaeon GW2011_AR20 archaeon AR20 3 GW2011_AR20
> > haloarchaeon 3A1-DGR haloarchaeon DGR 3 3A1-DGR
> > olei IMMIBHF-1T olei 1T 2 IMMIBHF-1T
> >
> > —
> > Reply to this email directly, view it on GitHub
> > <
>
#7 (comment)
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there are still some errors left, e.g. |
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Automatic tests start becoming useful, i.e. you might want to start reading their error messages: |
…hm_traits_microbiome into update_original_csv
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why are you doing that: You should NOT remove rows in this PR! |
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Sp. does not stands for the specie name. Sp. is just the abbreviation for Species. Because the exact name of the species are not known Sp. was written in the species column. That is the reason, why it is considered as unclassified. Guitar did the same in his Rcode, as he excluded rows with Sp. |
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splitted the genus names from the species names in the species column and all unclassified species i.e sp. were substituted to an empty space, but will later on be removed from the database.