Harvard:Biophysics 101/2007/Notebook:Resmi Charalel/2007-4-19
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(New page: ==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 w...) |
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==Issues== | ==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. | + | *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== | ||
| + | <pre> | ||
| + | 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 | ||
Revision as of 22:16, 18 April 2007
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
