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Update annotatedHitFasta.py #19

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Update annotatedHitFasta.py #19

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9 changes: 4 additions & 5 deletions bin/annotatedHitFasta.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,12 +97,12 @@ def extract_and_output(ace_id, ace_id_to_taxonomy, ace_id_to_proteome_file, curr
num_written = 0
# import code; code.interact(local=locals())
for record in SeqIO.parse(StringIO.StringIO(stdout), 'fasta'):
output_fh.write('>%s_%s %s\n' % (ace_id, record.id, taxonomy))
output_fh.write('%s\n' % record.seq)
output_fh.write('>%s_%s %s\n%s\n' % (ace_id, record.id, taxonomy, record.seq))
num_written += 1

if num_written != len(current_protein_ids):
import code; code.interact(local=locals())
import code
code.interact(local=locals())
raise Exception("Unexpected number of proteins retrieved from fasta file!")


Expand All @@ -128,11 +128,10 @@ def extract_and_output(ace_id, ace_id_to_taxonomy, ace_id_to_proteome_file, curr
if current_ace_id is not None and ace_id != current_ace_id:
# if the ACE ID has changed, then fxtract the proteins from the last ACE ID's faa file, adding the taxonomy to the ID line and print the now annotated fasta file
extract_and_output(current_ace_id, ace_id_to_taxonomy, ace_id_to_proteome_file, current_protein_ids, output_fh)
current_ace_id = ace_id
current_protein_ids = [protein_id]
else:
current_ace_id = ace_id
current_protein_ids.append(protein_id)
current_ace_id = ace_id

if current_ace_id is None:
raise Exception("No sequences parsed from aligned fasta file, it seems")
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