Release: v0.2.0

.gitignore

@@ -3,6 +3,10 @@
 /build
 erl_crash.dump
 
+# ensure that only minimum for JS NPM package is present in the dist dir.
 /dist/*
 !/dist/index.mjs
 !/dist/package.json
+!/dist/README.md
+
+.DS_Store

CHANGELOG.md

@@ -0,0 +1,26 @@
+# Changelog
+
+## 0.2.0
+
+### CLI
+
+-   Renamed `silent-mutate` to `clean`
+-   Added the `count` command.[^1] This command counts the number of restriction sites within a provided sequence.
+    _note: this does not consider CDS like `clean` does. It assesses the whole sequence._
+-   Added the `calts` command.[^1] This command prints alternate codons for a provided codon.
+-   Added new second-level subcommands for commands which do not return sequences:
+    -   `list` - Any actions which return information about the object being queried. E.g. alternates for a codon.
+    -   `parse` - Any actions to check the result of parsing an expression or formatted string. E.g. restriction strings/presets.
+    -   `count` - Any actions which return a number, or some form of count.
+
+### API Additions
+
+-   Added the `core/restriction` module for parsing and producing restriction sites.
+-   Added the `actions/presets` module for parsing presets.
+
+### Signature changes
+
+-   `sequence.raw` >>> `sequence.unwrap`
+-   Module `commands/restriction` >>> `commands/restriction_mutate`
+
+[^1]: Usage can be found in the package `README.md` or in the `--help` menu of the CLI.

ROADMAP.md

@@ -3,9 +3,34 @@
 This file can be used to track my progress.
 When I complete something, I will timestamp it so you can see if I am still working hard on this project.
 
--   [ ] Create the api for restriction site analysis
-    -   [ ] Be able to take in custom restriction sites with a specific parseable format
-    -   [ ] Be able to take in a DNA sequence and return the number of restriction sites
+## Checklists
+
+### Digestion Analysis - Restriction Enzymes - Construct Assembly
+
+-   [ ] API for restriction site analysis
+    -   [x] Be able to parse restriction sites from a specific format (link to docs later)
+    -   [x] Count # of restriction sites in sequence
+    -   [ ] Perform digestion simulation
+    -   [ ] Analyse sticky ends
+    -   [ ] Perform Golden Gate Assembly simulation
+        -   [ ] Graphical simulation
+        -   [ ] Actual processing to output
     -   [ ] Have a standard library of common restriction enzymes for synthetic biology standards (MoClo, BioBrick, etc.)
+        -   [ ] User-customizable list of restriction enzymes (e.g. `~/.config/dnalg/presets.toml`)
 -   [x] Create the sequence silent mutator to get rid of enzyme cut sites.
-    -   [ ] Make it get rid of every site, not just the first
+    -   [x] Make it get rid of every site, not just the first
+
+### Logs
+
+-   [ ] Use a sqlite db to record past jobs (`dnalg jobs`)
+    -   [ ] `clear` subcommand with the ability to choose number to remove from the head (`dnalg jobs --clear [INT]`)
+
+### Parsing Files
+
+-   [x] Parse FASTA and GenBank files
+-   [ ] Parse .dna files (SnapGene)
+
+### Outputs
+
+-   [ ] Utility function to convert DnaSequence information to a FASTA output format.
+    -   Still debating if .gb should be an output format.

dist/package.json

@@ -1,6 +1,6 @@
 {
     "name": "dnalg",
-    "version": "0.1.4",
+    "version": "0.2.0",
     "description": "A DNA manipulation library written in Gleam.",
     "main": "index.mjs",
     "bin": {

gleam.toml

@@ -1,5 +1,5 @@
 name = "dnalg"
-version = "0.1.4"
+version = "0.2.0"
 
 # Fill out these fields if you intend to generate HTML documentation or publish
 # your project to the Hex package manager.
@@ -14,6 +14,7 @@ target = "javascript"
 [documentation]
 pages = [
 	{ title = "Primitives", path = "ref/primitives.html", source = "./pages/primitives.md" },
+	{ title = "Reference", path = "ref/reference.html", source = "./pages/reference.md" },
 	{ title = "Roadmap", path = "roadmap.html", source = "./ROADMAP.md" },
 ]
 
@@ -26,9 +27,11 @@ gleam_javascript = ">= 0.13.0 and < 1.0.0"
 gleam_erlang = ">= 0.28.0 and < 1.0.0"
 stdin = ">= 1.1.4 and < 2.0.0"
 gleam_community_ansi = ">= 1.4.1 and < 2.0.0"
+term_size = ">= 1.0.1 and < 2.0.0"
 
 [dev-dependencies]
 gleeunit = ">= 1.0.0 and < 2.0.0"
+pprint = ">= 1.0.4 and < 2.0.0"
 
 [javascript]
 typescript_declarations = true

manifest.toml

@@ -4,6 +4,7 @@
 packages = [
   { name = "argv", version = "1.0.2", build_tools = ["gleam"], requirements = [], otp_app = "argv", source = "hex", outer_checksum = "BA1FF0929525DEBA1CE67256E5ADF77A7CDDFE729E3E3F57A5BDCAA031DED09D" },
   { name = "filepath", version = "1.0.0", build_tools = ["gleam"], requirements = ["gleam_stdlib"], otp_app = "filepath", source = "hex", outer_checksum = "EFB6FF65C98B2A16378ABC3EE2B14124168C0CE5201553DE652E2644DCFDB594" },
+  { name = "glam", version = "2.0.1", build_tools = ["gleam"], requirements = ["gleam_stdlib"], otp_app = "glam", source = "hex", outer_checksum = "66EC3BCD632E51EED029678F8DF419659C1E57B1A93D874C5131FE220DFAD2B2" },
   { name = "gleam_community_ansi", version = "1.4.1", build_tools = ["gleam"], requirements = ["gleam_community_colour", "gleam_stdlib"], otp_app = "gleam_community_ansi", source = "hex", outer_checksum = "4CD513FC62523053E62ED7BAC2F36136EC17D6A8942728250A9A00A15E340E4B" },
   { name = "gleam_community_colour", version = "1.4.0", build_tools = ["gleam"], requirements = ["gleam_json", "gleam_stdlib"], otp_app = "gleam_community_colour", source = "hex", outer_checksum = "795964217EBEDB3DA656F5EB8F67D7AD22872EB95182042D3E7AFEF32D3FD2FE" },
   { name = "gleam_erlang", version = "0.28.0", build_tools = ["gleam"], requirements = ["gleam_stdlib"], otp_app = "gleam_erlang", source = "hex", outer_checksum = "BE551521F708DCE5CB954AFBBDF08519C1C44986521FD40753608825F48FFA9E" },
@@ -12,9 +13,11 @@ packages = [
   { name = "gleam_stdlib", version = "0.41.0", build_tools = ["gleam"], requirements = [], otp_app = "gleam_stdlib", source = "hex", outer_checksum = "1B2F80CB1B66B027E3198A2FF71EF3F2F31DF89ED97AD606F25FD387A4C3C1EF" },
   { name = "gleeunit", version = "1.2.0", build_tools = ["gleam"], requirements = ["gleam_stdlib"], otp_app = "gleeunit", source = "hex", outer_checksum = "F7A7228925D3EE7D0813C922E062BFD6D7E9310F0BEE585D3A42F3307E3CFD13" },
   { name = "glint", version = "1.1.0", build_tools = ["gleam"], requirements = ["gleam_community_ansi", "gleam_community_colour", "gleam_stdlib", "snag"], otp_app = "glint", source = "hex", outer_checksum = "A3F1B7C665FD216BE6A886D56537F0E095FB07DF62146074109270B798F8CEC4" },
+  { name = "pprint", version = "1.0.4", build_tools = ["gleam"], requirements = ["glam", "gleam_stdlib"], otp_app = "pprint", source = "hex", outer_checksum = "C310A98BDC0995644847C3C8702DE19656D6BCD638B2A8A358B97824379ECAA1" },
   { name = "simplifile", version = "2.2.0", build_tools = ["gleam"], requirements = ["filepath", "gleam_stdlib"], otp_app = "simplifile", source = "hex", outer_checksum = "0DFABEF7DC7A9E2FF4BB27B108034E60C81BEBFCB7AB816B9E7E18ED4503ACD8" },
   { name = "snag", version = "0.3.0", build_tools = ["gleam"], requirements = ["gleam_stdlib"], otp_app = "snag", source = "hex", outer_checksum = "54D32E16E33655346AA3E66CBA7E191DE0A8793D2C05284E3EFB90AD2CE92BCC" },
   { name = "stdin", version = "1.1.4", build_tools = ["gleam"], requirements = ["gleam_stdlib"], otp_app = "stdin", source = "hex", outer_checksum = "04C04035F2A4CEEFB023837249649CD25F9A9CF5A45F9947C4D0462428A4677D" },
+  { name = "term_size", version = "1.0.1", build_tools = ["gleam"], requirements = ["gleam_stdlib"], otp_app = "term_size", source = "hex", outer_checksum = "D00BD2BC8FB3EBB7E6AE076F3F1FF2AC9D5ED1805F004D0896C784D06C6645F1" },
   { name = "thoas", version = "1.2.1", build_tools = ["rebar3"], requirements = [], otp_app = "thoas", source = "hex", outer_checksum = "E38697EDFFD6E91BD12CEA41B155115282630075C2A727E7A6B2947F5408B86A" },
 ]
 
@@ -26,5 +29,7 @@ gleam_javascript = { version = ">= 0.13.0 and < 1.0.0" }
 gleam_stdlib = { version = ">= 0.34.0 and < 2.0.0" }
 gleeunit = { version = ">= 1.0.0 and < 2.0.0" }
 glint = { version = ">= 1.1.0 and < 2.0.0" }
+pprint = { version = ">= 1.0.4 and < 2.0.0" }
 simplifile = { version = ">= 2.2.0 and < 3.0.0" }
 stdin = { version = ">= 1.1.4 and < 2.0.0" }
+term_size = { version = ">= 1.0.1 and < 2.0.0" }

pages/reference.md

@@ -0,0 +1,26 @@
+# General Reference
+
+-   [Restriction Site Formatting](#restriction-site-formatting)
+
+## Restriction Site Formatting
+
+Restriction sites are parsed using the following rules:
+
+-   `AGCT` characters are read into the consensus sequence and validated;
+-   `N` characters are ignored;
+-   `^` characters signify the cute site;
+-   All other characters are ignored.
+
+So, parsing a restriction string such as these: `ACGT^CG` and `ACGTCGN^NN` will yield:
+
+```
+ACGT^CG         recognition: ACGTCG
+                length: 6
+                cut_index: 4 (cuts 4 bases after the first base of the recognition site)
+
+ACGTCGN^NN      recognition: ACGTCG
+                length: 6
+                cut_index: 7
+```
+
+Quite simple!