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#lollipops A simple 'lollipop' mutation diagram generator that tries to make things simple and easy by automating as much as possible. It uses the [Pfam API](http://pfam./help#tabview=tab9) to retrieve domains and colors, and the [BioMart API](http://www./) to translate HGNC Gene Symbols into Uniprot/SwissProt Accession number. If variant changes are provided, it will also annotate them to the diagram using the "lollipops" markers that give the tool it's name. ##Example Basic usage is just the gene symbol (ex: ``TP53``) and a list of mutations (ex: ``R273C R175H T125 R248Q``) ./lollipops TP53 R273C R175H T125 R248Q  More advanced usage allows for per-mutation color (e.x. sample type) and size specification (i.e. denoting number of samples), along with text labels and more: ./lollipops -labels TP53 R248Q#7f3333@131 R273C R175H T125@5  ##Usage Usage: ``lollipops [options] {-U UNIPROT_ID | GENE_SYMBOL} [PROTEIN CHANGES ...]`` Where **GENE_SYMBOL** is the official human HGNC gene symbol. This will use the BioMart API to lookup the **UNIPROT_ID**. To skip the lookup or use other species, specify the UniProt ID with -U (e.g. ``-U P04637`` for TP53) ####Protein changes Currently only point mutations are supported, and may be specified as: <AMINO><CODON><AMINO><#COLOR><@COUNT> Only CODON is required, and AMINO tags are not parsed. Synonymous mutations are denoted if the first AMINO tag matches the second AMINO tag, or if the second tag is not present. Otherwise the non-synonymous mutation color is used. The COLOR tag will override using the #RRGGBB style provided. The COUNT tag can be used to scale the lollipop marker size so that the area is exponentially proportional to the count indicated. Examples: R273C -- non-synonymous mutation at codon 273 T125@5 -- synonymous mutation at codon 125 with "5x" marker sizing R248Q#00ff00 -- green lollipop at codon 248 R248Q#00ff00@131 -- green lollipop at codon 248 with "131x" marker sizing |
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