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Import FASTA file broken #10

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dnbenso opened this issue Feb 26, 2024 · 0 comments
Open

Import FASTA file broken #10

dnbenso opened this issue Feb 26, 2024 · 0 comments

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@dnbenso
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dnbenso commented Feb 26, 2024

Hi Hans

The new way of formatting a fasta dictionary from the input fasta file seems to be broken.

The output CSV file contains some strange chars like : "('FASTA_HEADER'," where FASTA_HEADER is the name of the sequence. The extra comma is a problem in a CSV file.

The sequence also has some chars on the end that shouldn't be there. I think it's the result of a tuple being formatted as a string and then split into a dictionary.
There are also a few array slices when writing the CSV file: chromosome[1::] that seem redundant.

Functions responsible are formatted and generate_dictionary. It looks like it might be an unintended consequence of attempting to speed up the code.

This should be simple to fix.

Kind regards
Derek
WANTED.csv

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