diff options
| author | Jonathan DeMasi <jonathan.demasi@colorado.edu> | 2019-06-17 22:47:00 -0600 |
|---|---|---|
| committer | Jonathan DeMasi <jonathan.demasi@colorado.edu> | 2019-06-17 22:47:00 -0600 |
| commit | aa21a9b15802a5c5392fab4486d5b351ee249494 (patch) | |
| tree | 4ca14595cf350169b5a38cbdc713862a9154a7d7 | |
| parent | 1abbe71dfaa852e92248f0d97b6178d67df2071f (diff) | |
| download | snippets-aa21a9b15802a5c5392fab4486d5b351ee249494.tar snippets-aa21a9b15802a5c5392fab4486d5b351ee249494.tar.gz snippets-aa21a9b15802a5c5392fab4486d5b351ee249494.tar.bz2 snippets-aa21a9b15802a5c5392fab4486d5b351ee249494.tar.lz snippets-aa21a9b15802a5c5392fab4486d5b351ee249494.tar.xz snippets-aa21a9b15802a5c5392fab4486d5b351ee249494.tar.zst snippets-aa21a9b15802a5c5392fab4486d5b351ee249494.zip | |
helps to have the right imports
| -rwxr-xr-x | ncbi/dbsnp/dbsnp.py | 4 |
1 files changed, 1 insertions, 3 deletions
diff --git a/ncbi/dbsnp/dbsnp.py b/ncbi/dbsnp/dbsnp.py index 07d51fa..491fce9 100755 --- a/ncbi/dbsnp/dbsnp.py +++ b/ncbi/dbsnp/dbsnp.py @@ -1,8 +1,8 @@ #!/usr/bin/env python3 -import sys import time from Bio import Entrez +import xml.etree.ElementTree as ET DEBUG = True @@ -65,7 +65,6 @@ is better / more efficient. def get_abstracts(results): abstracts_list = [] for start in range(0, int(results["Count"]), 1): - end = min(int(results["Count"]), start + 1) # print("Going to download record %i to %i" % (start+1, end)) fetch_handle = Entrez.efetch(db="pubmed", rettype="abstract", retmode="xml", retstart=start, @@ -83,7 +82,6 @@ def get_abstracts(results): def get_abstracts_from_list(pmids_list): abstracts_list = [] - pmids_abstracts_dict = {} for each_pmid in pmids_list: fetch_handle = Entrez.efetch(db="pubmed", id=each_pmid, retmode='xml') data = fetch_handle.read() |