Harvard:Biophysics 101/2007/Notebook:Resmi Charalel/2007-4-19

Issues

• I think I have an appropriate algorithm for deriving keywords and printing some PMIDs. However, I keep getting this weird error message that says my spacing is incorrect and when I follow the given instructions, I get the same error. - Somehow this error disappeared.

Program So Far

from Bio import PubMed
from Bio import Medline
import string

disease = a.name

search_term = "Review[ptyp] "+disease
#print search_term

review_ids = PubMed.search_for(search_term)

rec_parser = Medline.RecordParser()
medline_dict = PubMed.Dictionary(parser = rec_parser)

count = 1

for did in review_ids[0:5]:
    cur_record = medline_dict[did]
    print '\n', count, ')  ', string.rstrip(cur_record.title), cur_record.authors, string.strip(cur_record.source)
    count=count+1

def extract_allelic_variant_data(str):
        pmid = get_text(v.getElementsByTagName("Mim-reference_pubmedUID")[0].getElementsByTagName("Mim-text_text")[0].childNodes)
        print pmid
        key_source = PubMed.search_for(pmid)
        key_rec = medline_dict[0]
        keywords = get_text(key_rec.getElementsByTagName("MeshHeading")[0].childNodes)
        print keywords