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"description": "[](https://zenodo.org/badge/latestdoi/204058054)\n[](https://pypi.python.org/pypi/WoRMStools)\n[](https://anaconda.org/urosas/wormstools)\n\n# WoRMStools\n\n\nFeatures:\n\n- [x] get up-to-date information from [WoRMS database](http://www.marinespecies.org)\n- [x] Terminal-based scripts\n\nSoftware requierements:\n* Python 3\n\n#### Installation\n\nBy using `pip`:\n\n```python\npip install wormstools\n```\n\nUsing `git` (Optional):\n\n```Shell\ngit clone https://github.com/Ulises-Rosas/WoRMStools.git\ncd WoRMStools\npython3 setup.py install\n```\n\n### AphiaID\n\nWe can obtain the species ID which WoRMS database identify a given species (i.e. aphiaID). If this ID is not known, then species cannot be validated or continue with downstream procedures. Therefore, to know species aphiaID is an important step towards getting metadata inside WoRMS database.\n\nLet's suppose we have the following a list of species stored at [species.txt](https://github.com/Ulises-Rosas/WoRMStools/blob/master/species.txt):\n\n```Shell\ncat species.txt\n```\n\n```\nConus roosevelti\nLatirus hemphilli\nFavartia peasei\nLolliguncula panameusis\nPholoides tuberculata\n```\nWe can obtain their aphiaIDs by running:\n```Shell\nworms species.txt -id\n```\nBy default `worms` uses its input to name all outputs, however this can be modified with `--out` option. Since we did not specify any output name, by default the output name is `species_worms_aphiaID.tsv` and is contains the following:\n\n```Shell\nspecies\taphiaIDs\tObs\nConus roosevelti\t429945\t\nLatirus hemphilli\t447141\t\nFavartia peasei\t738152\t\nLolliguncula panameusis\t\tRecord not found in WoRMS\nPholoides tuberculata\t\tRecord not found in WoRMS\n```\n\n### Validate names\n\nCurrently accepted name according to WoRMS for each species can be obtained with the option `-val`. The output, when using this option, has the following columns: **species**, **validated names** and **obs**. If there were species that cannot be validated through WoRMS, it is stated on the **obs** column. \n\nExample:\n```Shell\nworms species.txt -val\n```\nBy default the output name is `species_worms_val.tsv` and is contains the following:\n```\nspecies\tvalidated names\tObs\nConus roosevelti\tConus tiaratus\t\nLatirus hemphilli\tPustulatirus hemphilli\t\nFavartia peasei\tFavartia peasei\t\nLolliguncula panameusis\tLolliguncula (Lolliguncula) panamensis\t\nPholoides tuberculata\t\tRecord not found in WoRMS\n```\n\n### Synonyms\n\nSynonyms of each species can be obtained with the option `-syn`. This option is aphiaID-dependent, which means that it obtains synonyms if there is any available aphiaID for each given species, including non-accepted ones. The output, when using this option, has the following columns: **species**, **synonyms** and **obs**. If there was a species that are not found in WoRMS its validated name is taken and stated on the **obs** column. Furthermore, if this species cannot be validated\\*, it is also stated in the **obs** column.\n\nExample:\n```Shell\nworms species.txt -syn\n```\nBy default the output name is `species_worms_syn.tsv` and is contains the following:\n```\nspecies\tsynonyms\tObs\nConus roosevelti\t\t\nLatirus hemphilli\t\t\nFavartia peasei\tMurex foveolatus, Murex peasei\t\nLolliguncula (Lolliguncula) panamensis\tLolliguncula panamensis, Lolliguncula tydeus\tDeprecated name: Lolliguncula panameusis\nPholoides tuberculata\t\tRecord not found in WoRMS\n```\n\n*\\*While species that does not have an aphiaID can be either validated in order to get an aphiaID or simply skipped, it is highly recomendable to introduce a list of validated species (see how [here](https://github.com/Ulises-Rosas/WoRMStools#validate-names)).*\n\n### Taxonomic rank\n\nDifferent taxonomical categories can obtained with the option `--at`. This option is aphiaID-dependent, which means that it obtains taxonomical categories if there is any aphiaID available for each given species, including non-accepted ones. The output, when using this option, varies according to introduced values into `--at` option (see example). The structure of column names, however, has the following structure: **\\[Taxa\\]** + **species** + **obs**. If there was a species that are not found in WoRMS its validated name is taken and stated on the **obs** column. Furthermore, if this species cannot be validated\\*, it is also stated in the **obs** column.\n\nExample:\n```Shell\nworms species.txt --at Class Family\n```\nBy default the output name is `species_worms_ranks.tsv` and is contains the following:\n```\nClass\tFamily\tSpecies\tObs\nGastropoda\tConidae\tConus roosevelti\t\nGastropoda\tFasciolariidae\tLatirus hemphilli\t\nGastropoda\tMuricidae\tFavartia peasei\t\nCephalopoda\tLoliginidae\tLolliguncula (Lolliguncula) panamensis\tdeprecated name: Lolliguncula panameusis\n\t\tPholoides tuberculata\tRecord not found in WoRMS\n```\n\nFinally, this option can be used together with all above options.\n\n*\\*While species that does not have an aphiaID can be either validated in order to get an aphiaID or simply skipped, it is highly recomendable to introduce a list of validated species (see how [here](https://github.com/Ulises-Rosas/WoRMStools#validate-names)).*\n\n### Usage within python3\n\nThe way `WoRMStools` is used inside python3 resemble pretty much as the usage in the terminal we have already seen:\n\n```python3\n# import worms class\nfrom wormstools.core_worms import Worms\n\n# get aphiaID\nWorms(taxon = 'Conus roosevelti').aphiaID\n\n# validate name\nWorms(taxon = 'Conus roosevelti').taxamatch()\n\n# get synonyms\nWorms(taxon = 'Favartia peasei').get_synonyms()\n\n# get an specific taxonomic rank\nWorms(taxon = 'Favartia peasei').get_rank(rank = 'Family')\n```\n\n\n\n",
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