Add FASTA sequence import option

EnzymeFunctionInitiative / EST

Programs for creating Sequence Similarity Networks and wrappers for pipeline submission on a torque cluster

GNU General Public License v3.0

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Add FASTA sequence import option #18

Closed nilsoberg closed 4 months ago

nilsoberg commented 4 months ago

To test, use something like

perl get_sequence_ids.pl --efi-config $EFI_CONFIG --efi-db $EFI_DB --output-dir test_new --mode fasta --fasta test_data/PF05544_sp.fasta
perl import_fasta.pl --uploaded-fasta test_data/PF05544_sp.fasta --output-dir test_new

1ndy commented 4 months ago

Some small things:

seq_mapping.tab should have a header
could import_stats.json be pretty printed? Just for readability

nilsoberg commented 4 months ago

I will add the pretty print to import_stats.json in a separate commit.