def get_description(record: Record, feature: CDSFeature, type_: str,
options: ConfigType, mibig_result: List[clusterblast.results.MibigEntry]) -> str:
"Get the description text of a CDS feature"
urls = {
"blastp": ("http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&"
"PROGRAM=blastp&BLAST_PROGRAMS=blastp&QUERY=%s&"
"LINK_LOC=protein&PAGE_TYPE=BlastSearch") % feature.translation,
"mibig": "",
"transport": "",
"smcog_tree": ""
}
genomic_context_url = "http://www.ncbi.nlm.nih.gov/projects/sviewer/?" \
"Db=gene&DbFrom=protein&Cmd=Link&noslider=1&"\
"id=%s&from=%s&to=%s"
if mibig_result:
assert feature.region
region_number = feature.region.get_region_number()
mibig_homology_file = os.path.join(options.output_dir, "knownclusterblast",
"region%d" % region_number,
feature.get_accession() + '_mibig_hits.html')
generate_html_table(mibig_homology_file, mibig_result)
urls["mibig"] = mibig_homology_file[len(options.output_dir) + 1:]
if type_ == 'transport':
urls["transport"] = ("http://blast.jcvi.org/er-blast/index.cgi?project=transporter;"
"program=blastp;database=pub/transporter.pep;"
"sequence=sequence%%0A%s") % feature.translation
urls["context"] = genomic_context_url % (record.id,
max(feature.location.start - 9999, 0),
min(feature.location.end + 10000, len(record)))
if options.smcog_trees:
for note in feature.notes: # TODO find a better way to store image urls
if note.startswith('smCOG tree PNG image:'):
urls["smcog_tree"] = note.split(':')[-1]
break
asf_notes = generate_asf_tooltip_section(record, feature)
go_notes = generate_pfam2go_tooltip(record, feature)
pfam_notes = generate_pfam_tooltip(record, feature)
tigr_notes = generate_tigr_tooltip(record, feature)
urls["searchgtr"] = searchgtr_links.get("{}_{}".format(record.id, feature.get_name()), "")
template = html_renderer.FileTemplate(path.get_full_path(__file__, "templates", "cds_detail.html"))
ec_numbers = ""
ec_number_qual = feature.get_qualifier("EC_number")
if isinstance(ec_number_qual, list):
ec_numbers = ",".join(ec_number_qual)
return template.render(feature=feature, ec_numbers=ec_numbers, go_notes=go_notes,
asf_notes=asf_notes, pfam_notes=pfam_notes, tigr_notes=tigr_notes,
record=record, urls=urls)
def get_description(
record: Record, feature: CDSFeature, type_: str, options: ConfigType,
mibig_result: List[clusterblast.results.MibigEntry]) -> str:
"Get the description text of a CDS feature"
blastp_url = "http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&" \
"PROGRAM=blastp&BLAST_PROGRAMS=blastp&QUERY=%s&" \
"LINK_LOC=protein&PAGE_TYPE=BlastSearch" % feature.translation
genomic_context_url = "http://www.ncbi.nlm.nih.gov/projects/sviewer/?" \
"Db=gene&DbFrom=protein&Cmd=Link&noslider=1&"\
"id=%s&from=%s&to=%s"
template = '<span class="svgene-tooltip-bold">%s</span><br>\n' % feature.product or feature.get_name(
)
template += 'Locus-tag: %s; Protein-ID: %s<br>\n' % (feature.locus_tag,
feature.protein_id)
if feature.get_qualifier('EC_number'):
template += "EC-number(s): %s<br>\n" % ",".join(
feature.get_qualifier('EC_number'))
for gene_function in feature.gene_functions:
template += "%s<br>\n" % str(gene_function)
template += "Location: %d - %d<br><br>\n" % (
feature.location.start + 1, # 1-indexed
feature.location.end)
if mibig_result:
cluster_number = feature.cluster.get_cluster_number()
mibig_homology_file = os.path.join(
options.output_dir, "knownclusterblast",
"cluster%d" % cluster_number,
feature.get_accession() + '_mibig_hits.html')
generate_html_table(mibig_homology_file, mibig_result)
mibig_path = mibig_homology_file[len(options.output_dir) + 1:]
template += '<br><a href="%s" target="_new">MiBIG Hits</a><br>\n' % mibig_path
if type_ == 'transport':
url = "http://blast.jcvi.org/er-blast/index.cgi?project=transporter;" \
"program=blastp;database=pub/transporter.pep;" \
"sequence=sequence%%0A%s" % feature.translation
template += '<a href="%s" target="_new">TransportDB BLAST on this gene<br>' % url
key = record.id + "_" + feature.get_name()
if key in searchgtr_links:
url = searchgtr_links[key]
template += '<a href="%s" target="_new">SEARCHGTr on this gene<br>\n' % url
template += '<a href="%s" target="_new">NCBI BlastP on this gene</a><br>\n' % blastp_url
context = genomic_context_url % (
record.id, max(feature.location.start - 9999,
0), min(feature.location.end + 10000, len(record)))
template += """<a href="%s" target="_new">View genomic context</a><br>\n""" % context
if options.smcogs_trees:
for note in feature.notes: # TODO find a better way to store image urls
if note.startswith('smCOG tree PNG image:'):
url = note.split(':')[-1]
entry = '<a href="%s" target="_new">View smCOG seed phylogenetic tree with this gene</a>\n'
template += entry % url
break
template += generate_asf_tooltip_section(record, feature)
go_notes = generate_pfam2go_tooltip(record, feature)
if go_notes:
template += '<br><span class="bold">Gene Ontology terms for PFAM domains:</span><br>\n' \
'%s<br><br>\n' % "<br>".join(go_notes)
clipboard_fragment = """<a href="javascript:copyToClipboard('%s')">Copy to clipboard</a>"""
template += "AA sequence: %s<br>\n" % (clipboard_fragment %
feature.translation)
template += "Nucleotide sequence: %s<br>\n" % (clipboard_fragment %
feature.extract(record.seq))
return "".join(char for char in template if char in string.printable)
