import numpy as np
def read_fasta( fasta_file, split_char=' ', id_field=0 ):
'''
Reads in fasta file containing multiple sequences.
Returns dictionary holding multiple sequences or only single
sequence, depending on input file
In order to retrieve the protein identifier, the header is split
after split_char and the field at position id_field is chosen as
identifier.
'''
sequences = dict()
with open( fasta_file, 'r' ) as fasta_f:
for line in fasta_f:
# get uniprot ID from header and create new entry
if line.startswith('>'):
uniprot_id = line.replace('>', '').strip().split(split_char)[id_field]
sequences[ uniprot_id ] = ''
else:
# repl. all whie-space chars and join seqs spanning multiple lines
sequences[ uniprot_id ] += ''.join( line.split() ).upper()
sequences = sorted(sequences.items(), key=lambda kv: len( sequences[kv[0]] ) )
identifier, seqs = zip(*sequences)
seqs = [ np.asarray([seq]) for seq in seqs ]
#seqs = np.concatenate( seqs )
print(seqs)
return { "inputs": seqs,
"metadata":
{ "id": identifier }
}
