def map(self, context):
config = context.getJobConf()
tmp_dir = config.get("job.local.dir")
xref_dbs = config.get("fasta.blastdb").split(",")
cur_key, ids, scores = blast.blast_top_hits(context.getInputKey(),
context.getInputValue(), xref_dbs, tmp_dir)
cur_val = dict(ids=ids, scores=scores)
context.emit(cur_key, json.dumps(cur_val))
def map(self, context):
config = context.getJobConf()
tmp_dir = config.get("job.local.dir")
xref_dbs = config.get("fasta.blastdb").split(",")
cur_key, ids, scores = blast.blast_top_hits(context.getInputKey(),
context.getInputValue(),
xref_dbs, tmp_dir)
cur_val = dict(ids=ids, scores=scores)
context.emit(cur_key, json.dumps(cur_val))
def process_blast(rec, db_refs, tmp_dir, blast_cmd):
"""Run a BLAST writing results to shared files.
"""
cur_id, id_info, score_info = blast.blast_top_hits(rec.id,
rec.format("fasta"),
db_refs, tmp_dir,
blast_cmd)
print cur_id
return {"cmp_id": id_info, "cmp_score": score_info, "cur_id": cur_id}
def mapper(key, rec):
tmp_dir = os.environ["job_local_dir"]
xref_dbs = os.environ["fasta_blastdb"].split(",")
parts = rec.split("\t")
if len(parts) == 3: # remove extra initial tab if present
parts = parts[1:]
title, seq = rec.split("\t")
rec_id = title.split()[0]
cur_key, ids, scores = blast.blast_top_hits(rec_id, seq, xref_dbs, tmp_dir)
cur_val = dict(ids=ids, scores=scores)
yield cur_key, cur_val
def mapper(key, rec):
tmp_dir = os.environ["job_local_dir"]
xref_dbs = os.environ["fasta_blastdb"].split(",")
parts = rec.split("\t")
if len(parts) == 3: # remove extra initial tab if present
parts = parts[1:]
title, seq = rec.split("\t")
rec_id = title.split()[0]
cur_key, ids, scores = blast.blast_top_hits(rec_id, seq, xref_dbs, tmp_dir)
cur_val = dict(ids=ids, scores=scores)
yield cur_key, cur_val
def process_blast(rec, db_refs, file_info, tmp_dir, blast_cmd):
"""Run a BLAST writing results to shared files.
"""
cur_id, id_info, score_info = blast.blast_top_hits(rec.id, rec.format("fasta"),
db_refs, tmp_dir, blast_cmd)
with fupdate_lock:
id_file, score_file = file_info
for fname, fvals in [(id_file, id_info), (score_file, score_info)]:
with open(fname, "a") as out_handle:
writer = csv.writer(out_handle, dialect='excel-tab')
writer.writerow([cur_id] + fvals)
print cur_id
def process_blast(rec, db_refs, file_info, tmp_dir):
"""Run a BLAST writing results to shared files.
"""
cur_id, id_info, score_info = blast.blast_top_hits(rec.id,
rec.format("fasta"),
db_refs, tmp_dir)
with fupdate_lock:
id_file, score_file = file_info
for fname, fvals in [(id_file, id_info), (score_file, score_info)]:
with open(fname, "a") as out_handle:
writer = csv.writer(out_handle, dialect='excel-tab')
writer.writerow([cur_id] + fvals)
print cur_id
def process_blast(rec, db_refs, tmp_dir, blast_cmd):
"""Run a BLAST writing results to shared files.
"""
cur_id, id_info, score_info = blast.blast_top_hits(rec.id, rec.format("fasta"), db_refs, tmp_dir, blast_cmd)
print cur_id
return {"cmp_id": id_info, "cmp_score": score_info, "cur_id": cur_id}
