Consolidate all functionality into one library

.devcontainer/Dockerfile

@@ -0,0 +1,23 @@
+# Base image for PyEasyHLA development.
+
+# This image is the basis of the project's devcontainer as well.
+
+ARG PYTHON_VERSION="3.13.3-bookworm"
+
+FROM python:${PYTHON_VERSION} AS base
+
+RUN apt update -y && apt upgrade -y
+
+# Install the vendored software.
+ARG INSTANTCLIENT_BASIC="instantclient-basic-linux.x64-23.7.0.25.01.zip"
+# The value of ORACLE_HOME depends on the instant client used as it will
+# install to a path like ".../instantclient_23_7" where the version numbers
+# will vary.
+ARG ORACLE_HOME="/opt/oracle/instantclient_23_7"
+
+ENV ORACLE_HOME=${ORACLE_HOME} \
+    LD_LIBRARY_PATH=${ORACLE_HOME}:$LD_LIBRARY_PATH
+
+COPY vendor/${INSTANTCLIENT_BASIC} /tmp/vendor/
+RUN unzip /tmp/vendor/${INSTANTCLIENT_BASIC} -d /opt/oracle &&\
+    rm -rf /tmp/vendor

.devcontainer/devcontainer.json

@@ -1,7 +1,7 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/ubuntu
 {
-	"image": "python:3.10-slim",
+	"image": "python:3.13.3-bookworm",
 	"features": {
 		"ghcr.io/devcontainers/features/git:1": {
 			"ppa": true,
@@ -19,7 +19,9 @@
 	"updateRemoteUserUID": true,
 	"containerEnv": {
 		"WORKON_HOME": "${containerWorkspaceFolder}/.venv",
-		"PYTHONPATH": "${containerWorkspaceFolder}"
+		"PYTHONPATH": "${containerWorkspaceFolder}",
+		"ORACLE_HOME": "/opt/oracle/instantclient",
+		"LD_LIBRARY_PATH": "/opt/oracle/instantclient"
 	},
 	"onCreateCommand": {
 		"update apt": [
@@ -38,7 +40,20 @@
 			"install",
 			"--no-install-recommends",
 			"-y",
-			"openssh-client"
+			"openssh-client",
+			"libaio-dev",
+			"unzip"
+		],
+		"install Instant Client": [
+			"/usr/bin/env",
+			"bash",
+			"${containerWorkspaceFolder}/.devcontainer/install_instant_client.bash"
+		],
+		"install Ruby": [
+			"/usr/bin/apt",
+			"install",
+			"-y",
+			"ruby"
 		]
 	},
 	"postAttachCommand": {

.devcontainer/install_instant_client.bash

@@ -0,0 +1,7 @@
+#! /usr/bin/env bash
+
+mkdir /tmp/vendor
+cp vendor/instantclient*.zip /tmp/vendor/
+unzip /tmp/vendor/instantclient*.zip -d /opt/oracle
+ln -s /opt/oracle/instantclient_* /opt/oracle/instantclient
+rm -rf /tmp/vendor

original_ruby_scripts/01.5_hla_reduce_by_g.rb

@@ -0,0 +1,62 @@
+Dir.chdir "config"
+['a','b','c'].each do |letter|
+    data = []
+    source_filename = "hla_#{letter}_std.csv"
+    puts "reading #{source_filename}..."
+    File.open(source_filename) do |file|
+        file.each_line do |line|
+            data << line.strip.split(',')
+        end
+    end
+
+    data.sort! do |a,b|
+        tmpa = a[0].split(':')
+        tmpb = b[0].split(':')
+        (tmpa[0] != tmpb[0] ? tmpa[0].split('*')[1].to_i <=> tmpb[0].split('*')[1].to_i :
+            (tmpa[1] != tmpb[1] ? tmpa[1].to_i <=> tmpb[1].to_i :
+            (tmpa[2] != tmpb[2] ? tmpa[2].to_i <=> tmpb[2].to_i :
+            tmpa[3].to_i <=> tmpb[3].to_i )))
+    end
+
+    #File.open("hla_std_#{letter}_test.csv", 'w') do |file|
+        #data.each do |d|
+            #file.puts d.join(',')
+        #end
+    #end
+
+    data.each_with_index do |orig, i|
+        next if(orig == nil)
+        orig_allele = orig[0]
+        orig_seq = orig[1 .. 2]
+        match_count = 0
+        data.each_with_index do |row, j|
+            next if(j <= i or row == nil)
+            if(orig_seq == row[1 .. 2])
+                match_count += 1
+                puts "Reducing #{row[0]} into #{orig_allele}"
+                data[j] = nil
+            end
+        end
+        if(match_count > 0)
+            gallele = orig_allele.split(':')
+            gallele = gallele[0 .. 2] if(gallele.size > 3)
+            gallele = gallele.join(':') + 'G'
+            puts "Turning #{orig_allele} into #{gallele}"
+            orig[0] = gallele
+        end
+
+    end
+
+    data.delete(nil)
+
+    reduced_filename = "hla_#{letter}_std_reduced.csv"
+    puts "writing #{reduced_filename}"
+    File.open(reduced_filename, 'w') do |file|
+        data.each do |d|
+            file.puts d.join(',')
+        end
+    end
+
+    File.delete(source_filename)
+    system('zip', "hla_#{letter}_std_reduced.zip", reduced_filename)
+end

original_ruby_scripts/01_hla_fasta_parse.rb

@@ -0,0 +1,176 @@
+#!/usr/bin/ruby
+#
+# This program downloads the newest version of hla_nuc.fasta and then
+# processes it, creating three standard files for a, b, and c.  Any sequence
+# that doesn't seem to align properly will be rejected.
+# The alignment algorithm I'm using is the dirtiest possible.
+# This program requires the bioruby library
+
+
+#require 'bio'
+require 'fileutils'
+require 'net/http'
+require 'uri'
+require 'date'
+require 'digest'
+require 'json'
+
+#scores the sequence according to how many characters don't match.  An
+#alignment of 0 means a perfect match.  We optimize it by assuming anything under 20 is probably
+#a match.
+def score(seq, align)
+	maxscore = align.size
+	maxseq = -1;
+
+	0.upto(seq.size - align.size) do |i|
+		score = align.size
+		0.upto(align.size - 1) do |j|
+			if(align[j] == seq[i + j])
+				score -= 1
+			end
+		end
+
+		if(score < maxscore)
+			maxscore = score
+			maxseq = i
+			if(maxscore < 20)
+				return [maxscore, seq[maxseq, align.size]]
+			end
+		end
+	end
+    if(maxscore > 30)
+#        puts maxscore
+#        puts align
+#        puts seq[maxseq, align.size]
+    end
+	return [maxscore, seq[maxseq, align.size]]
+end
+
+#Exon sequences to compare against(used for scoring)
+a_exon2_align='GCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACG'
+a_exon3_align='GTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCGGTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGG'
+b_exon2_align='GCTCCCACTCCATGAGGTATTTCTACACCTCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCTCAGTGGGCTACGTGGACGACACCCAGTTCGTGAGGTTCGACAGCGACGCCGCGAGTCCGAGAGAGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCGGAACACACAGATCTACAAGGCCCAGGCACAGACTGACCGAGAGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGCCG'
+b_exon3_align='GGTCTCACACCCTCCAGAGCATGTACGGCTGCGACGTGGGGCCGGACGGGCGCCTCCTCCGCGGGCATGACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACGGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCGGAGAGCCTACCTGGAGGGCGAGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGACAAGCTGGAGCGCGCTG'
+c_exon2_align='GCTCCCACTCCATGAAGTATTTCTTCACATCCGTGTCCCGGCCTGGCCGCGGAGAGCCCCGCTTCATCTCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGTCCGAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGCCG'
+c_exon3_align='GGTCTCACACCCTCCAGTGGATGTGTGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACCGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCGGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCGG'
+
+Dir.chdir "config"
+filename = 'hla_nuc.fasta'
+timestamp_path = filename + '.mtime'
+
+repo_path = "https://raw.githubusercontent.com/ANHIG/IMGTHLA"
+
+# Find latest release at https://github.com/ANHIG/IMGTHLA/releases
+hla_nuc_version = File.read('hla_nuc.fasta.version.txt').strip
+puts "attempting to download version #{hla_nuc_version} from #{repo_path}"
+
+uri = URI.parse("#{repo_path}/#{hla_nuc_version}/hla_nuc.fasta")
+response = Net::HTTP.get_response(uri)
+md5 = Digest::MD5.new
+Net::HTTP.get_response(uri) do |response|
+	response.value  # Raise error if not 200 response code.
+	File.open(filename, 'w') do |file|
+		response.read_body do |segment|
+			file.write(segment)
+			md5 << segment
+		end
+	end
+end
+checksum_report = md5.hexdigest + '  ' + filename + "\n"
+File.write('hla_nuc.fasta.checksum.txt', checksum_report)
+puts "Parsing " + filename;
+
+hla_a = []
+hla_b = []
+hla_c = []
+
+diff_reject = 32
+
+
+#file = Bio::FastaFormat.open(filename)
+fasta = []
+enu=[]
+File.open(filename) do |file|
+  file.each_line do |line|
+    if(line =~ /^>/)
+      fasta.push(enu)
+      enu = [line.strip, '']
+    else
+      enu[1] += line.strip
+    end
+  end
+  fasta.push(enu)
+end
+
+fasta.delete_if{|e| e== []}
+
+bar_width = 50
+fasta.each_with_index do |entry, index| #for each fasta sequence
+	#title = entry.definition[entry.definition.index(' ') + 1 .. entry.definition.size]
+    title = entry[0].split(' ')[1]
+	type = title[0, 1]
+	data = entry[1]
+	progress_bar = ('#' * (index.to_f/fasta.length*bar_width) + '.' * bar_width)
+	progress_bar = progress_bar[0...bar_width]
+
+	data.tr!("\n\t\r ", '') #get rid of whitespace
+	message = ''
+
+	if(type == 'A')
+		exon2 = score(data, a_exon2_align)
+		exon3 = score(data, a_exon3_align)
+		if(exon2[0] <= diff_reject and exon3[0] <= diff_reject)
+            message = "Approving " + title + ":  " + exon2[0].to_s + " " + exon3[0].to_s
+			hla_a.push( [title, exon2[1], exon3[1]] )
+		else
+			message = "***Rejecting " + title + ":  " + exon2[0].to_s + " " + exon3[0].to_s
+		end
+	elsif(type == 'B')
+		exon2 = score(data, b_exon2_align)
+		exon3 = score(data, b_exon3_align)
+		if(exon2[0] <= diff_reject and exon3[0] <= diff_reject)
+            message = "Approving " + title + ":  " + exon2[0].to_s + " " + exon3[0].to_s
+			hla_b.push( [title, exon2[1], exon3[1]] )
+		else
+			message = "***Rejecting " + title + ":  " + exon2[0].to_s + " " + exon3[0].to_s
+		end
+	elsif(type == 'C')
+		exon2 = score(data, c_exon2_align)
+		exon3 = score(data, c_exon3_align)
+		if(exon2[0] <= diff_reject and exon3[0] <= diff_reject)
+            message = "Approving " + title + ":  " + exon2[0].to_s + " " + exon3[0].to_s
+			hla_c.push( [title, exon2[1], exon3[1]] )
+		else
+			message = "***Rejecting " + title + ":  " + exon2[0].to_s + " " + exon3[0].to_s
+		end
+	end
+	print "\r" + progress_bar + ' ' + message + ".     "
+end
+puts "\r" + '#' * bar_width + ' Completed.' + ' ' * 18
+
+#file.close
+
+#Lets sort, just to make things easier for our eyes
+hla_a.sort!
+hla_b.sort!
+hla_c.sort!
+
+File.open('hla_a_std.csv', 'w') do |file|
+	hla_a.each do |entry|
+		file.puts entry[0] + "," + entry[1] + "," + entry[2]
+	end
+end
+
+File.open('hla_b_std.csv', 'w') do |file|
+	hla_b.each do |entry|
+		file.puts entry[0] + "," + entry[1] + "," + entry[2]
+	end
+end
+
+File.open('hla_c_std.csv', 'w') do |file|
+	hla_c.each do |entry|
+		file.puts entry[0] + "," + entry[1] + "," + entry[2]
+	end
+end
+
+File.delete(filename)