diff options
| -rwxr-xr-x | workflows/tools/pubseq-fetch-data.py | 6 |
1 files changed, 6 insertions, 0 deletions
diff --git a/workflows/tools/pubseq-fetch-data.py b/workflows/tools/pubseq-fetch-data.py index 3f5e6cf..23c4dea 100755 --- a/workflows/tools/pubseq-fetch-data.py +++ b/workflows/tools/pubseq-fetch-data.py @@ -12,6 +12,7 @@ Fetch metadata (JSON) from PubSeq and optionally the FASTA files. IDs can be passed in on the command line or in a file. """) +parser.add_argument('--fasta', action='store_true', help='Also fetch FASTA records') parser.add_argument('--out', type=str, help='Directory to write to', required=True) parser.add_argument('--ids', type=str, help='File with ids', required=False) @@ -36,5 +37,10 @@ for id in ids: mr = requests.get(m_url) with open(dir+"/"+id+".json","w") as outf: outf.write(mr.text) + if args.fasta: + fa_url = r.json()[0]['fasta'] + fr = requests.get(fa_url) + with open(dir+"/"+id+".fa","w") as outf: + outf.write(fr.text) else: raise Exception(f"Can not find record for {id}") |