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from Bio import Medline
import re
import glob

colon = re.compile(r"(.*:.*)")
pmids = {}
with open("assets/mybib.nbib") as handle:
    records = Medline.parse(handle)
    for record in records:
        #if (pmids.has_key(record['PMID'])): //has_key removed in python3
        if not 'PMID' in record:
            print(record["TI"])
            continue
        if record['PMID'] in pmids:
            continue
        pmids[record['PMID']] = 1  
        f = open("_pubs/" + record['PMID'] + ".md", 'w')
        f.write("---\n")
        f.write("pmid: " + record['PMID'] + "\n")
        f.write("layout: default\n")
        match = colon.match(record['TI'])
        if match:
            record['TI'] = match.group(1).replace(":", ":")
        f.write("title: " + record['TI'] + "\n")
        f.write("authors: ")
        authors = record['AU']
        #if (record.has_key('CN')): //has_key removed in python3
        if 'CN' in record:
            authors = authors + record['CN']
        f.write(', '.join(authors) + "\n")
        f.write("pubdate: " + record['DP'] + "\n")
        f.write("volume: " + record['VI'] + "\n")
        #if (record.has_key('IP')): //has_key removed in python3
        if 'IP' in record:
            f.write("issue: " + record['IP'] + "\n")
        else:
            f.write("issue: " + "\n")
        if 'PG' not in record:
            record['PG'] = "N/A"
        f.write("pages: " + record['PG'] + "\n")
        f.write("journal: " + record['TA'] + "\n")
        f.write("---\n")
        f.close()


    

    




BAMnostic: an OS-agnostic toolkit for genomic sequence analysis

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