def map_to_refseq(seqids):
uniprot_mapping = uniprot.sequentially_convert_to_uniprot_id(seqids, "func.cache.json")
uniprot_ids = uniprot_mapping.values()
pairs = uniprot.batch_uniprot_id_mapping_pairs("ACC", "P_REFSEQ_AC", uniprot_ids)
mapping = {}
for seqid in seqids:
if seqid in uniprot_mapping:
uniprot_id = uniprot_mapping[seqid]
for pair in pairs:
if uniprot_id == pair[0]:
mapping[seqid] = pair[1]
os.remove("func.cache.json")
return mapping
def map_to_refseq(seqids):
uniprot_mapping = uniprot.sequentially_convert_to_uniprot_id(
seqids, 'func.cache.json')
uniprot_ids = uniprot_mapping.values()
pairs = uniprot.batch_uniprot_id_mapping_pairs(
'ACC', 'P_REFSEQ_AC', uniprot_ids)
mapping = {}
for seqid in seqids:
if seqid in uniprot_mapping:
uniprot_id = uniprot_mapping[seqid]
for pair in pairs:
if uniprot_id == pair[0]:
mapping[seqid] = pair[1]
os.remove('func.cache.json')
return mapping
NP_000508.1 NP_001018081.3
""".split()
pairs = uniprot.batch_uniprot_id_mapping_pairs("P_REFSEQ_AC", "ACC", seqids)
pprint.pprint(pairs, indent=2)
# Example 3 - sequential identifier mapping to UniProt
# identifiers using robust but slow method
seqids = """
EFG_MYCA1 YP_885981.1 CpC231_1796
""".split()
mapping = uniprot.sequentially_convert_to_uniprot_id(seqids, "cache.json")
uniprot_seqids = mapping.values()
# Example 4 - get UniProt metadata
uniprot_data = uniprot.batch_uniprot_metadata(uniprot_seqids, "cache2.txt")
pprint.pprint(uniprot_data, indent=2)
for l in open("cache2.txt"):
print l.strip()
uniprot.write_fasta("example.output.fasta", uniprot_data, uniprot_seqids)
""".split()
pairs = uniprot.batch_uniprot_id_mapping_pairs(
'P_REFSEQ_AC', 'ACC', seqids)
pprint.pprint(pairs, indent=2)
# Example 3 - sequential identifier mapping to UniProt
# identifiers using robust but slow method
seqids = """
EFG_MYCA1 YP_885981.1 CpC231_1796
""".split()
mapping = uniprot.sequentially_convert_to_uniprot_id(
seqids, 'cache.json')
uniprot_seqids = mapping.values()
# Example 4 - get UniProt metadata
uniprot_data = uniprot.batch_uniprot_metadata(
uniprot_seqids, 'cache2.txt')
pprint.pprint(uniprot_data, indent=2)
for l in open('cache2.txt'):
print l.strip()
uniprot.write_fasta('example.output.fasta', uniprot_data, uniprot_seqids)
