Metadata-Version: 2.1
Name: oceania-query-fasta
Version: 0.1.0
Summary: A small package to query data from the OceanIA services
Home-page: https://gitlab.com/Inria-Chile/oceania/oceania-query-fasta
Author: Inria Chile
Author-email: desarrollo@inria.cl
License: UNKNOWN
Description: # OceanIA query
        
        A small package to query data from the OceanIA services
        
        ## Install
        
        Install using `pip`
        
        ```bash
        > pip install oceania-query
        ```
        
        ## Usage
        
        The library may be used directly as a command line tool or imported as a python package
        
        ### Command line
        
        In the command line:
        
        ```bash
        > oceania query-fasta <key> <query_file> <output_format> <output_file>
        ```
        
        For more information information:
        
        ```bash
        > oceania query-fasta -h
        Usage: oceania query-fasta [OPTIONS] <key> <query_file> <output_format> <output_file>
        
          Extract secuences from a fasta file in the OceanIA Storage.
        
          <key> object key in the OceanIA storage
          <query_file> CSV file containing the values to query.
                       Each line represents a sequence to extract in the format "sequence_id,start,end,type"
                       "sequence_id" sequence ID
                       "start" start index position of the sequence to be extracted
                       "end" end index position of the sequence to extract
                       "type" type of the sequence to extract
                              options are ["raw", "complement", "reverse_complement"]
                              type value is optional, if not provided default is "raw"
          <output_format> results format
                          options are ["csv", "fasta"]
          <output_file> name of the file to write the results
        ```
        
        #### Example
        
        ```bash
        > oceania query-fasta data/raw/tara/OM-RGC_v2/assemblies/TARA_A100000171.scaftig.gz query.csv csv example.output.csv
        ```
        
        query.csv:
        ```csv
        TARA_A100000171_G_scaffold48_1,10,50,complement
        TARA_A100000171_G_scaffold48_1,10,50,raw
        TARA_A100000171_G_scaffold48_1,10,50,reverse_complement
        TARA_A100000171_G_scaffold181_1,0,50
        TARA_A100000171_G_scaffold181_1,100,200
        TARA_A100000171_G_scaffold181_1,200,230
        ```
        
        ### As a python package
        
        ```python
        from oceania import OceaniaClient
        
        # Create a client instance
        oceania_client = OceaniaClient()
        
        # Execute a query
        oceania_client.get_secuences_from_fasta_to_file(key, positions, output_format, output_file)
        ```
        
        #### Example
        ```python
        from oceania import OceaniaClient
        
        oceania_client = OceaniaClient()
        
        key = "data/raw/tara/OM-RGC_v2/assemblies/TARA_A100000171.scaftig.gz"
        positions = [
            ["TARA_A100000171_G_scaffold48_1", 10, 50, "complement"],
            ["TARA_A100000171_G_scaffold48_1", 10, 50],
            ["TARA_A100000171_G_scaffold48_1", 10, 50, "reverse_complement"],
            ["TARA_A100000171_G_scaffold181_1", 0, 50],
            ["TARA_A100000171_G_scaffold181_1", 100, 200],
            ["TARA_A100000171_G_scaffold181_1", 200, 230],
        ]
        
        oceania_client.get_secuences_from_fasta_to_file(
            key,
            positions,
            "csv",
            "test_output.csv"
        )
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Utilities
Requires-Python: >=3.6
Description-Content-Type: text/markdown
