diff options
Diffstat (limited to 'more_functions.py')
| -rwxr-xr-x | more_functions.py | 15 |
1 files changed, 3 insertions, 12 deletions
diff --git a/more_functions.py b/more_functions.py index e304ddc..ef43e30 100755 --- a/more_functions.py +++ b/more_functions.py @@ -25,8 +25,8 @@ def getabstracts(gene,query): """ 1. esearch -db pubmed -query ... -- searches PubMed for the gene + keyword query, returns matching record IDs 2. efetch -format uid -- fetches just the PMIDs (unique identifiers) from the search results - 3. look up PMIDs in the local PubMed mirror archive (avoids hitting NCBI servers - for the full abstracts) -- archive stores gzipped XML by PMID path + 3. xfetch -db pubmed -- looks up those PMIDs in the local PubMed mirror (avoids hitting NCBI servers + for the full abstracts) 4. xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText -- extracts PMID, title, and abstract text from the XML into tab-separated fields 5. sed "s/-/ /g" -- replaces hyphens with spaces (so hyphenated gene names match keyword searches later) @@ -45,16 +45,7 @@ def getabstracts(gene,query): pmid_list = pmids.split("\n") print(f" PMIDs ({len(pmid_list)}): {' '.join(pmid_list)}") # Step 2: fetch abstracts from local mirror - # fetch-pubmed is not shipped with edirect 25.x, so we look up - # the archive files directly: PMID 30990365 -> 30/99/03/30990365.xml.gz - fetch_script = ( - "for uid in " + pmids.replace("\n", " ").replace("'", "") + "; do " - "p=$(printf '%.2s/%.2s/%.2s' \"$uid\" \"${uid#??}\" \"${uid#????}\"); " - "f=" + pubmed_path + "/Archive/${p}/${uid}.xml.gz; " - "[ -f \"$f\" ] && zcat \"$f\"; " - "done" - ) - abs_cmd = fetch_script \ + abs_cmd = "echo '" + pmids.replace("'", "") + "' | xfetch -db pubmed" \ + " | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText | sed \"s/-/ /g\"" print(f" popen: {abs_cmd}") abstracts = os.popen(abs_cmd).read() |