pubmed-searchx 0.1.6

Pubmed Search

Example

Installation

    pip install pubmed_searchx     

Running from command line

    python -m pubmed_searchx PATH_TO_GENE_LIST PATH_TO_TERM_LIST {-r: Optional for using hreflink pubmed} {-d PATH_TO_RESULT_DIR}  

Example:

Input:

gene_test.txt:

REST
CJKG
CORIN
EGF1

term_test.txt:

depression
migraine

    python -m pubmed_searchx -g gene_test.txt -t term_test.txt -d "./"

Output example: Folder: REST_CJKG_CORIN_EGF1_depression_{time_stamp}/

• pubmed_id_results.csv:

Gene	Pubmed_Ids
REST	35216520,35231204,31376646,34555652,32739332,34388482,35522984,34709765,25785575,30761967,23856279,28488270,30979801,17653294,30962366,24256499,15167093,27185312,21677641,24313703
CJKG	No_Hit
CORIN	26667411,7759658,36097420,30148170,32257992,37895290,7798487,2766190,1825625,3383412
EGF1	15892860

(With -r option, the pubmed_id becomes: 35216520(https://pubmed.ncbi.nlm.nih.gov/35216520))

• cout_hist.csv:

Gene	#Hits
REST	20
CJKG	0
CORIN	10
EGF1	1

• json_dir/*.json: (e.g. CORIN.json)

[ { "authors": "Monroe SM;Harkness KL", "title": "Major Depression and Its Recurrences: Life Course Matters.", "year": "2022", "pubmed_id": "35216520" }, .... ]