Homework 1

A repository for the first Homework of "Análise e Sequencias Biologicas"

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Program usage

python main.py -db «database» -q «query» -o «output»

OR

python main.py --database «database» --query «query» --output «output»

Program Description

A non-interactive Python script to retrieve sequences that takes user input database and search query. It uses the history EntrezAPI's feature and the output is in FASTA format and written to STDOUT.

Program Objectives

Facilitate the process of NCBI's api handling

Requirements

Python Standard Libraries

Structure:

1. Input Argument Parsing
2. Esearch (NCBI database search)
3. Esearch output Parsing (XML file)
4. Efetch (Gets the corresponding sequences)
5. Main function (Coordenates everything)