Pharo Script of the Day: Colorizing nucleotides

Some days ago I experimented a bit to colorize a random DNA sequence given an alphabet and the desired sequence size, with a little help of BioSmalltalk. This is what I've got:

| text attributes |
text := ((BioSequence forAlphabet: BioDNAAlphabet) randomLength: 6000) sequence asText.
attributes := Array new: text size.
1 to: text size do: [ : index |
  attributes at: index put: { 
  (TextColor color: (BioDNAAlphabet colorMap at: (text at: index))) }  ].
text runs: (RunArray newFrom: attributes).
text.

I built a color map for every nucleotide, based on the alphabet size. This is because in biological sequences (proteins, DNA, RNA) you have a different set of letters.

I should say I don't like the final result. Specially the lack of column alignment:

This seems to persist even trying other attributes

| text attributes |
text := ((BioSequence forAlphabet: BioDNAAlphabet) randomLength: 6000) sequence asText.
attributes := Array new: text size.
1 to: text size do: [ : index |
  attributes at: index put: { 
  (TextColor color: (BioDNAAlphabet colorMap at: (text at: index))) .
  (TextKern kern: 4) }  ].
text runs: (RunArray newFrom: attributes).
text. 

Maybe efforts in Bloc would make it easier for aligning text.

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Pharo Script of the Day: Parsing Gene Ontology terms

Today a script from the Bioinformatics world, accessing an EBI REST service called QuickGO, to retrieve Gene Ontology information. For the first script I use the NeoJSON library, and return a Pharo dictionary which we can inspect interactively through the Inspector:

(NeoJSONReader on: (ZnClient new
 accept: ZnMimeType applicationJson;
 url: 'http://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0005623,GO:0017071,GO:0030680';
 get) readStream) next at: 'results'.

You should only provide the GO identifiers delimited by commas. For the second script we just can join a Collection to build the comma delimited String. The API also includes a service to retrieve a graph image with the terms involved in the query, so we can also try retrieving a different type of information:

| ids |
ids := #('GO:0005623' 'GO:0017071' 'GO:0030680').
(ImageReadWriter formFromStream: (ZnClient new
 accept: ZnMimeType imagePng;
 url: 'http://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/' , (ids joinUsing: ',') , '/chart';
 get) readStream) asMorph openInWindow.

Previously, EBI returned XML content in oboxml format, and the following Pharo script used XML-Parser and XPath (doc) libraries to parse GO terms. I include the script for those discovering Smalltalk and wish to know how it would be using XPath:

#('GO:0005623' 'GO:0017071' 'GO:0030680') collect: [ : goTerm |
 | quickGO |
 quickGO := 'http://www.ebi.ac.uk/QuickGO-Old/GTerm?id={1}&format=oboxml' format: { goTerm }.
 goTerm -> (XPath 
  for: 'normalize-space(/obo/term/name/text())' 
  in: (XMLDOMParser on: (ZnEasy get: quickGO) contents) parseDocument) ].

You've got similar code in Perl and Java so you can compare:

.

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