Changed the names of the parameters

fix on vanilla ID mapping
iquasere · Jul 7, 2023 · 652ce7a · 652ce7a
1 parent 853cf2b
commit 652ce7a
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -39,7 +39,7 @@ jobs:
       - name: Load Docker image
         run: docker load --input /tmp/upimapi.tar
       - name: IDs inputted through TXT file (comma-separated)
-        run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/ids.csv -rd resources_directory --no-annotation -cols 'Entry&KEGG&Interacts with'"
+        run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/ids.csv -cols 'Entry&KEGG&Interacts with'"
 
   txt-file-newline-separated:
     runs-on: ubuntu-latest
@@ -53,7 +53,7 @@ jobs:
       - name: Load Docker image
         run: docker load --input /tmp/upimapi.tar
       - name: Full IDs inputted through TXT file (newline-separated)
-        run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/full_ids.txt -rd resources_directory --no-annotation"
+        run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/full_ids.txt"
 
   blast-file:
     runs-on: ubuntu-latest
@@ -67,7 +67,7 @@ jobs:
       - name: Load Docker image
         run: docker load --input /tmp/upimapi.tar
       - name: IDs inputted through BLAST file
-        run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/ids.blast -rd resources_directory --no-annotation --blast"
+        run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/ids.blast -rd resources_directory --blast"
 
   get-fasta-sequences:
     runs-on: ubuntu-latest
@@ -81,7 +81,7 @@ jobs:
       - name: Load Docker image
         run: docker load --input /tmp/upimapi.tar
       - name: Obtain FASTA sequences
-        run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/ids.csv -rd resources_directory --no-annotation --fasta"
+        run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/ids.csv -rd resources_directory --fasta"
 
   basic-id-mapping:
     runs-on: ubuntu-latest
@@ -94,7 +94,7 @@ jobs:
           path: /tmp
       - name: Load Docker image
         run: docker load --input /tmp/upimapi.tar
-      - name: Obtain FASTA sequences
+      - name: Perform basic ID mapping
         run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/ci/ids.csv -rd resources_directory --from 'UniProtKB AC/ID' --to 'EMBL/GenBank/DDBJ CDS'"
 
   full-workflow:

diff --git a/upimapi.py b/upimapi.py
@@ -91,10 +91,10 @@ def get_arguments():
     parser.add_argument(
         "-cols", "--columns", default=None, help="List of UniProt columns to obtain information from (separated by &)")
     parser.add_argument(
-        "--from", default="UniProtKB AC/ID", choices=from_fields.keys(),
+        "--from-db", default="UniProtKB AC/ID", choices=from_fields.keys(),
         help="Which database are the IDs from. If from UniProt, default is fine [UniProtKB AC/ID]")
     parser.add_argument(
-        "--to", default="UniProtKB", choices=to_fields.keys(),
+        "--to-db", default="UniProtKB", choices=to_fields.keys(),
         help="To which database the IDs should be mapped. If only interested in columns information "
              "(which include cross-references), default is fine [UniProtKB]")
     parser.add_argument(
@@ -346,7 +346,7 @@ def basic_idmapping_multiprocess(ids, output, from_db, to_db, step=1000, threads
 
 
 def get_valid_entries(ids):
-    job_id = submit_id_mapping("UniProtKB_AC-ID", "UniProtKB", ids)
+    job_id = submit_id_mapping("UniProtKB AC/ID", "UniProtKB", ids)
     r = get_id_mapping_results(job_id)
     valid_entries = [res["from"] for res in r.json()["results"] if '_' not in res["from"]]
     while r.links.get("next", {}).get("url"):
@@ -1355,16 +1355,16 @@ def upimapi():
         return
 
     if not args.skip_id_checking:
+        # UniProt's API now fails if outdated IDs or entry names are submitted. This function removes those IDs.
         ids, not_valid = get_valid_entries_multiprocess(ids, threads=args.threads)
-        # UniProt's API now fails if outdated IDs or entry names are submitted. This function removes those
         with open(f'{args.output}/valid_ids.txt', 'w') as f:
             f.write('\n'.join(ids))
         with open(f'{args.output}/not_valid_ids.txt', 'w') as f:
             f.write('\n'.join(not_valid))
 
     # Get UniProt information
     if not args.fasta:
-        # ID mapping through local information
+        # ID mapping through local SwissProt information
         if args.local_id_mapping:
             ids = set(ids) - set(local_id_mapping(
                 sp_ids, f'{args.resources_directory}/uniprot_sprot.dat', f'{args.resources_directory}/taxonomy.tsv',