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Update Curegen
authored
Apr 06, 2021
by
peguerin
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Curegen.md
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@@ -14,8 +14,7 @@ This table summarizes the command-line arguments which are using by `mkbdr cureg
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@@ -14,8 +14,7 @@ This table summarizes the command-line arguments which are using by `mkbdr cureg
|
`--fasta`
|
`-f`
| NA | path of the input faulty taxonomy barcodes sequences FASTA file |
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`--fasta`
|
`-f`
| NA | path of the input faulty taxonomy barcodes sequences FASTA file |
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`--output_prefix`
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`-o`
| NA | prefix of the output curation CSV file such as prefix.csv |
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`--output_prefix`
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`-o`
| NA | prefix of the output curation CSV file such as prefix.csv |
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`--database_globalnames`
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`-d`
| 'Fishbase Cache' | Name of the selected database from GlobalNames i.e. 'Catalogue of Life' or 'Fishbase Cache' |
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`--database_globalnames`
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`-d`
| 'Fishbase Cache' | Name of the selected database from GlobalNames i.e. 'Catalogue of Life' or 'Fishbase Cache' |
|
`--ncbi_taxdump`
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`-n`
| NA | path of NCBI taxonomy folder |
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`--ncbi_taxdump_load`
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`-l`
| NA | load NCBI taxonomy from NCBI taxonomy folder path |
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`--ncbi_taxdump_load`
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`-l`
| FALSE | load NCBI taxonomy from NCBI taxonomy folder path |
# Example of commands
# Example of commands
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@@ -47,7 +46,6 @@ It is possible to load local NCBI taxonomy files. Here we load `path/to/ncbi_tax
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@@ -47,7 +46,6 @@ It is possible to load local NCBI taxonomy files. Here we load `path/to/ncbi_tax
```
```
mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
--output_prefix "cure" \
--output_prefix "cure" \
--ncbi_taxdump path/to/ncbi_taxo \
--ncbi_taxdump_load
--ncbi_taxdump_load
```
```
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