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feat: Add I/O modules for reading and writing to files #10

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lsetiawan opened this issue Oct 17, 2024 · 1 comment
Open

feat: Add I/O modules for reading and writing to files #10

lsetiawan opened this issue Oct 17, 2024 · 1 comment

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@lsetiawan
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lsetiawan commented Oct 17, 2024

We need the following APIs for the python io, TBD whether to write this directly in Rust:

# Read the vector/matrix csv file
def read_csv():
    ...

# Read the newick tree text file... non-binary file
# should only contain newick tree string
def read_newick():
    ...

# Writes the vector/matrix to a csv file
def write_csv():
    ...

# Writes newick string to a text file
def write_newick():
    ...

# Read the nexus file... non-binary file
# NOTE: Stretch goal
def read_nexus():
    # Use biopython to read the nexus file
    ...

Biopython resource: https://biopython.org/docs/latest/Tutorial/chapter_phylo.html

@lsetiawan lsetiawan changed the title feat: Add I/O modules for newick string to nex files feat: Add I/O modules for reading and writing to files Dec 19, 2024
@madelinegordon
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Discussed - decided on using Python for I/O

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