diff options
Diffstat (limited to 'workflows/tools')
| -rwxr-xr-x | workflows/tools/pubseq-fetch-data.py | 30 |
1 files changed, 17 insertions, 13 deletions
diff --git a/workflows/tools/pubseq-fetch-data.py b/workflows/tools/pubseq-fetch-data.py index 23c4dea..2119fdf 100755 --- a/workflows/tools/pubseq-fetch-data.py +++ b/workflows/tools/pubseq-fetch-data.py @@ -31,16 +31,20 @@ if (len(ids)==0): for id in ids: print(id) - r = requests.get(f"http://covid19.genenetwork.org/api/sample/{id}.json") - if r: - m_url = r.json()[0]['metadata'] - 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}") + jsonfn = dir+"/"+id+".json" + if not os.path.exists(jsonfn): + r = requests.get(f"http://covid19.genenetwork.org/api/sample/{id}.json") + if r: + m_url = r.json()[0]['metadata'] + mr = requests.get(m_url) + with open(dir+"/"+id+".json","w") as outf: + outf.write(mr.text) + if args.fasta: + fastafn = dir+"/"+id+".fa" + if os.path.exists(fastafn): continue + fa_url = r.json()[0]['fasta'] + fr = requests.get(fa_url) + with open(fastafn,"w") as outf: + outf.write(fr.text) + else: + raise Exception(f"Can not find record for {id}") |