<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi all,</div><div class=""><br class=""></div><div class="">In putting together introductory notes for using the KGML Pathway class, I really noticed the lack of a method to identify/select an Element from the Pathway. To fill the glaring gap, I’d like to implement a method, along the following lines:</div><div class=""><br class=""></div><div class="">pathway = KGML_parser.read(filehandle)</div><div class=""><br class=""></div><div class=""># Elements are identified in KGML files by unique integers; overload to accept string or list</div><div class="">e = pathway.get_element(element_id)</div><div class="">e_mult = pathway.get_element([id1, id2])</div><div class=""><br class=""></div><div class=""># Restrict returned type of element to, say, compound by type argument</div><div class=""><div class=""><div class="">c1 = pathway.get_element(element_id, type=‘compound')</div><div class="">c_mult1 = pathway.get_element([id1, id2], type=‘compound')</div></div></div><div class=""><br class=""></div><div class=""># Also, specific methods such as get_compound fetch ‘compound’ elements, e.g. by calling get_element internally</div><div class=""><div class="">c2 = pathway.get_compound(element_id)</div><div class="">c_mult2 = pathway.get_compound([id1, id2])</div></div><div class=""><div class=""><div class=""><br class=""></div></div></div><div class=""># Names are more natural ways to represent elements, and are retrievable via KEGG.REST module functions</div><div class=""><div class=""># Elements are identified in KGML files by unique integers; overload to accept string or list</div><div class="">e = pathway.get_element_by_name(’name')</div><div class="">e_mult = pathway.get_element_by_name([’name1’, ’name2'])</div></div><div class=""><br class=""></div><div class=""><div class=""># And similar methods for retrieving compounds:</div><div class=""><div class="">c2 = pathway.get_compound_by_name(’name')</div><div class="">c_mult2 = pathway.get_compound_by_name([’name1’, ’name2'])</div></div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Before I make a start, does anyone on here have any comments/suggestions for the interface? I considered an index-like approach (pathway.element[’name’]), but I’d like the flexibility to provide a list of names/IDs - I can imagine circumstances where I’d want to highlight several elements.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">L.</div><div class=""><br class=""></div><div apple-content-edited="true" class="">
<span class="Apple-style-span" style="border-collapse: separate; font-size: 12px; border-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><div class="">-- </div><div class="">Leighton Pritchard</div><div class=""><a href="mailto:leightonpritchard@mac.com" class="">leightonpritchard@mac.com</a></div><div class="">gpg/pgp:0xDECACFFC</div></div><br class="Apple-interchange-newline"></span></span><br class="Apple-interchange-newline">
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