In [30]:

    

from screed.fasta import fasta_iter


    

In [18]:

    

with open("../outputs/rna/match_ortho.rna.moleculo.txt") as rna_mol_match:
    rna_mol_set = set([line.split(' ')[0] for line in rna_mol_match if line.strip()])

with open("../outputs/rna/match_ortho.rna.ref.txt") as rna_ref_match:
    rna_ref_set = set([line.split(' ')[0] for line in rna_ref_match if line.strip()])
    
with open("../outputs/rna/ortho.fa") as ortho_file:
    E = set([line.split(' ')[0][1:] for line in ortho_file if line.startswith('>')])


    

In [20]:

    

B = rna_mol_set & rna_ref_set


    

In [21]:

    

C = rna_mol_set - B


    

In [22]:

    

A = rna_ref_set - B


    

In [24]:

    

D = E - A - C - B


    

In [53]:

    

def write_output_fasta(outfile, seqfile, keys):
    n_written = 0
    with open(outfile, 'w') as output:
        with open(seqfile, 'r') as sequences:
            for seq in fasta_iter(sequences):
                if seq['name'] in keys:
                    output.write(">{name} {description}\n{sequence}\n".format(**seq))
                    n_written += 1
    return n_written


    

In [54]:

    

write_output_fasta("../outputs/rna/cobb/A-ref_rna.fa", "../outputs/rna/ortho.fa", A)
write_output_fasta("../outputs/rna/cobb/B-ref_rna_mol.fa", "../outputs/rna/ortho.fa", B)
write_output_fasta("../outputs/rna/cobb/C-mol_rna.fa", "../outputs/rna/ortho.fa", C)
write_output_fasta("../outputs/rna/cobb/D-only_rna.fa", "../outputs/rna/ortho.fa", D)


    

    
Out[54]:





3682

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