def test_html(self, file = sys.stdout):
print ("Content-Type: text/html\n")
# Add the bl sub-directory to the module path
# and the directory above to import the config file
sys.path.insert(0, "/d/user6/az001/bl/")
sys.path.insert(0, "/d/user6/az001/db/")
#*****************************************************************************************************************************************************************************************
# Grab the content of the form
form = cgi.FieldStorage()
accession = form.getvalue("accession")
gene_id = form.getvalue("gene_id")
product = form.getvalue("product")
location = form.getvalue("location")
entries = blapi.getAllEntries(accession = accession, gene_id = gene_id, product = product,location = location)
# Header and navigation
html = htmlutils.header()
html += htmlutils.navigation()
# Gene summary page table
html += "<h3>Gene Summary Table:</h3>\n"
html += "<div class='summary-page'>\n"
html += "<table class ='summary'>\n"
html += "<tr>\n"
html += "<th>Genbank Accession</th>\n"
html += "<th>Gene Identifier</th>\n"
html += "<th>Protein Product</th>\n"
html += "<th>Chromosomal Location</th>\n"
html += "</tr>\n"
for _ in entries:
html += "<tr>\n"
html += "<td><a href='http://student.cryst.bbk.ac.uk/cgi-bin/cgiwrap/az001/search.py?accession={}' method='get'>".format(_['accession'])+ _['accession']+ "</a></td>\n"
html += "<td>"+_['gene_id'] + "</td>\n"
html += "<td>"+_['product'] + "</td>\n"
html += "<td>"+_['location'] + "</td>\n"
html += "</tr>\n"
html += "</table>\n"
html += htmlutils.footer()
df2['Total Freq'] = df2['Codon'].map(entry['total_freq'])
df['Codon'] = df['Codon'].str.strip()
df2['Codon'] = df2['Codon'].str.strip()
df3 = df.merge(df2, left_on='Codon', right_on='Codon')
df3 = df3[['Codon', 'Freq', 'Total Freq']]
# Frequency of codon usage in chosen gene vs in chromosome six
html += "<h4 class= 'table-heading'>Codon usage frequencies in this gene vs in Chromosome Six </h4>\n"
html += "<table class= 'codon'>\n"
html += "<tr>\n"
html += "<th>Codon</th>\n"
html += "<th>Frequency</th>\n"
html += "<th>Total Frequency</th>\n"
for _ in range(0, len(df3)):
html += "<tr>\n"
html += "<td>" + df3['Codon'][_] + "</td>\n"
html += "<td>" + df3['Freq'][_] + "</td>\n"
html += "<td>" + df3['Total Freq'][_] + "</td>\n"
html += "</tr>\n"
html += "</table><!-- end of codon usage table -->\n"
# Footer
html += htmlutils.footer()
print(html)
def test_html(self, file=sys.stdout):
sys.path.insert(0, "/d/user6/az001/bl/")
sys.path.insert(0,
"/d/user6/az001/db/") #Config file saved in db folder
# Grab the content of the form
form = cgi.FieldStorage()
#***********************************************************************************************************************************************************************************************
# MAIN PROGRAMME FOR DETAIL PAGE
#***********************************************************************************************************************************************************************************************
accession = form.getvalue("accession")
enzyme = form.getvalue("rez")
entry = blapi.getEntry(accession, enzyme)
# Header and navigation
html = htmlutils.header()
html += htmlutils.navigation()
# detail table
html += htmlutils.detailtable()
html += "<td>" + entry['accession'] + "</td>\n"
html += "<td>" + entry['gene_id'] + "</td>\n"
html += "<td>" + entry['product'] + "</td>\n"
html += "<td>" + entry['location'] + "</td>\n"
html += "<td>" + entry['cds'] + "</td>\n"
html += "</tr>\n"
html += "</table>\n"
#Text area for Amino acid sequences
html += "<h4 class= 'table-heading'>Amino Acid Sequence:</h4>\n"
html += "<textarea class ='amino-acid' readonly>\n"
html += entry['protein_seq']
html += "</textarea>\n"
#**********************************************************
# DNA sequence and resitriction enzyme
#**********************************************************
html += "<h4 class= 'table-heading' >DNA Sequence: </h4>\n"
html += "<div class = 'dna-info'> Coding region has been highlighted. <br>By choosing a Retriction Enzyme, a star will appear in the DNA sequence below. This star will indicate that the Restriction Enzyme cuts at particular site.</div>\n"
html += "<form action='http://student.cryst.bbk.ac.uk/cgi-bin/cgiwrap/az001/search.py' method='get'>\n"
html += "<input type='hidden' id='accession' name='accession' value='" + accession + "'>\n"
#Restriction Enzyme table
html += "<table class = 'reztable'>\n"
html += "<tr>\n"
html += "<th>Restriction enzyme</th>\n"
html += "</tr>\n"
html += "<tr>\n"
html += "<td>" + entry['rez'] + "</td>\n"
html += "</tr>\n"
html += "</table>\n"
#drop down for restriction enzyme
html += " <select name = 'rez'>\n"
html += " <option value = 'Restriction enzyme list'>Choose Restriction enzyme</option>\n"
html += " <option value = 'EcoRI'>EcoRI</option>\n"
html += " <option value = 'BamHI'>BamHI</option>\n"
html += " <option value = 'BsuMI'>BsuMI</option>\n"
html += " <option value = 'KpnI'>KpnI</option>\n"
html += " <option value = 'EcoRV'>EcoRV</option>\n"
html += " <option value = 'SmaI'>SmaI</option>\n"
html += " <option value = 'MscI'>MscI</option>\n"
html += " </select>\n"
html += " <input type = 'submit' value = 'Submit'/>\n"
html += " </form>\n"
#DNA sequence with coding region highlighted
html += "<div id = 'dna-seq'>\n"
html += entry['dna_seq']
html += "</div>\n"
#******************************************************
#Total codon usasge in this Gene vs in chromosome 6
#******************************************************
dictlist = []
for key, value in entry['freq'].items():
cod = key
dictlist.append(cod)
df = pd.DataFrame()
df['Codon'] = dictlist
df['Freq'] = df['Codon'].map(entry['freq'])
dictlist2 = []
for key, value in entry['total_freq'].items():
cod = key
dictlist2.append(cod)
df2 = pd.DataFrame()
df2['Codon'] = dictlist2
df2['Total Freq'] = df2['Codon'].map(entry['total_freq'])
df['Codon'] = df['Codon'].str.strip()
df2['Codon'] = df2['Codon'].str.strip()
df3 = df.merge(df2, left_on='Codon', right_on='Codon')
df3 = df3[['Codon', 'Freq', 'Total Freq']]
# Frequency of codon usage in particular gene vs chromosome six
html += "<h4 class= 'table-heading'>Codon usage frequencies in this gene vs in Chromosome Six </h4>\n"
html += "<table class= 'codon'>\n"
html += "<tr>\n"
html += "<th>Codon</th>\n"
html += "<th>Frequency</th>\n"
html += "<th>Total Frequency</th>\n"
for _ in range(0, len(df3)):
html += "<tr>\n"
html += "<td>" + df3['Codon'][_] + "</td>\n"
html += "<td>" + df3['Freq'][_] + "</td>\n"
html += "<td>" + df3['Total Freq'][_] + "</td>\n"
html += "</tr>\n"
html += "</table>\n"
html += htmlutils.footer()