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changed uploadlists to ID Mapping in log messages & elsewhere
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deeenes committed Jun 10, 2023
1 parent e812067 commit 7455e32
Showing 1 changed file with 10 additions and 10 deletions.
20 changes: 10 additions & 10 deletions pypath/utils/mapping.py
Expand Up @@ -161,7 +161,7 @@

"""
Classes for reading and use serving ID mapping data from custom file,
function, UniProt, UniProt uploadlists, Ensembl BioMart,
function, UniProt, UniProt ID Mapping, Ensembl BioMart,
PRO (Protein Ontology), miRBase or pickle file.
"""

Expand Down Expand Up @@ -716,10 +716,10 @@ def _read_mapping_uniprot_list(
uniprot_id_type_a (str): Source ID type label as used in UniProt.
uniprot_id_type_b (str): Target ID type label as used in UniProt.
upload_ac_list (list): The identifiers to use in the query to
the uploadlists service. By default the list of all UniProt
the ID Mapping service. By default the list of all UniProt
IDs for the organism is used.
chunk_size (int): Number of IDs in one query. Too large queries
might fail, by default we include 10,000 IDs in one query.
might fail, by default we include 100,000 IDs in one query.
"""

chunk_size = (
Expand All @@ -733,7 +733,7 @@ def _read_mapping_uniprot_list(
upload_ac_list = sorted(upload_ac_list)

self._log(
'Querying the UniProt uploadlists service for ID translation '
'Querying the UniProt ID Mapping service for ID translation '
'data. Querying a list of %u IDs.' % len(upload_ac_list)
)

Expand All @@ -747,7 +747,7 @@ def _read_mapping_uniprot_list(
this_chunk = upload_ac_list[i * chunk_size:(i + 1) * chunk_size]

self._log(
'Request to UniProt uploadlists, chunk #%u with %u IDs.' % (
'Request to UniProt ID Mapping, chunk #%u with %u IDs.' % (
i,
len(this_chunk),
)
Expand Down Expand Up @@ -1673,7 +1673,7 @@ def check_loaded():
tbl_key = tbl_key_noorganism
tbl_key_rev = tbl_key_rev_noorganism

# for uniprot/uploadlists or PRO or array
# for uniprot/idmapping or PRO or array
# we create here the mapping params
this_param = input_cls(
id_type_a = _id_type,
Expand Down Expand Up @@ -2434,7 +2434,7 @@ def _map_ensp(
mapped_names = set()
ncbi_tax_id = ncbi_tax_id or self.ncbi_tax_id

# try first UniProt uploadlists
# try first UniProt ID Mapping
# then Ensembl BioMart
for id_type in ('ensp', 'ensp_biomart'):

Expand All @@ -2451,7 +2451,7 @@ def _map_ensp(

tax_ensp = '%u.%s' % (ncbi_tax_id, ensp)

# this uses UniProt uploadlists with STRING_ID
# this uses UniProt ID Mapping with STRING ID type
mapped_names = self._map_name(
name = tax_ensp,
id_type = 'ensp_string',
Expand All @@ -2475,7 +2475,7 @@ def _map_to_ensp(
mapped_names = set()
ncbi_tax_id = ncbi_tax_id or self.ncbi_tax_id

# try first UniProt uploadlists
# try first UniProt ID Mapping
# then Ensembl BioMart
for target_id_type in ('ensp', 'ensp_biomart'):

Expand All @@ -2490,7 +2490,7 @@ def _map_to_ensp(

if not mapped_names:

# this uses UniProt uploadlists with STRING_ID
# this uses UniProt ID Mapping with STRING type
mapped_names = self._map_name(
name = name,
id_type = id_type,
Expand Down

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