feat: add Orthanq wrappers for hla and virus applications

bio/orthanq/hla/candidates/environment.yaml

@@ -0,0 +1,2 @@
+dependencies:
+  - orthanq =1.1.0

bio/orthanq/hla/candidates/meta.yaml

@@ -0,0 +1,7 @@
+name: orthanq candidates hla
+description: |
+  Orthanq candidates hla subcommand generates candidate variants required for HLA quantification.
+  All required input is downloaded by following the instructions here: https://orthanq.github.io/docs/usage.html#preparation
+url: https://github.com/orthanq/orthanq
+authors:
+  - Hamdiye Uzuner

bio/orthanq/hla/candidates/test/Snakefile

@@ -0,0 +1,12 @@
+rule orthanq_candidates_hla:
+    input:
+        allele_freq="allele_freq.csv",
+        alleles="hla_alleles.fasta",
+        genome="genome.fasta",
+        xml="hla.xml"
+    output:
+        "candidates.vcf",
+    log:
+        "logs/orthanq_candidates/candidates_hla.log",
+    wrapper:
+        "master/bio/orthanq/hla/candidates"

bio/orthanq/hla/candidates/test/allele_freq.csv

@@ -0,0 +1,10 @@
+"","var","population","frequency"
+"1","A*01","Albania",0.1
+"2","A*01","Albania pop 2",0.0972
+"3","A*01","Albanian Kosovo",0.1542
+"4","A*01","Algeria pop 2",0.1225
+"5","A*01","Argentina Buenos Aires",0.119
+"6","A*01","Argentina Buenos Aires pop 2",0.101
+"7","A*01","Argentina Chiriguano",0.019
+"8","A*01","Argentina Corrientes",0.084
+"9","A*01","Argentina Cuyo Region",0.089

bio/orthanq/hla/candidates/test/genome.fasta

@@ -0,0 +1,52 @@
+>LN999604.1
+CAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGG
+CGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCA
+ACCTACGTAGGGTCCTTCATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGG
+TTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGTCCGCACGCACCCACCGGGACTCAG
+ATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCT
+GGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAG
+GGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGAGGAGGGTCGGGCAGGTCTCAGCCAC
+TGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGC
+CCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCA
+GAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAAT
+ATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGG
+ACGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCA
+CAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACTCCGAGACCCTTGTCCCGGGAGAGGCCCAGG
+CGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCGGGGCGGGGCT
+CGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACG
+TGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCT
+GAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCG
+GTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGCTGCGTGGACGGGCTCCGCAGATACCTGG
+AGAACGGGAAGGAGACGCTGCAGCGCACGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTATAGA
+TCTCCCGGGCTGGCCTCCCACAAGGAGGGGAGACAATTGGGACCAACACTAGAATATCACCCTCCCTCTG
+GTCCTGAGGGAGAGGAATCCTCCTGGGTTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCT
+GCTCTCTGACACAATTAAGGGATAAAATCTCTGAAGGAGTGACGGGAAGACGATCCCTCGAATACTGATG
+AGTGGTTCCCTTTGACACCGGCAGCAGCCTTGGGCCCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTT
+CACACTCAATGTGTGTGGGGGTCTGAGTCCAGCACTTCTGAGTCTCTCAGCCTCCACTCAGGTCAGGACC
+AGAAGTCGCTGTTCCCTTCTCAGGGAATAGAAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGG
+TTCTGTGCTCTCTTCCCCATCCCGGGTGTCCTGTCCATTCTCAAGATGGCCACATGCGTGCTGGTGGAGT
+GTCCCATGACAGATGCAAAATGCCTGAATTTTCTGACTCTTCCCGTCAGACCCCCCCAAGACACATATGA
+CCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGAT
+CACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCA
+GGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCC
+ATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGGGTAAGGAGGGAGATGGGGGTGTCAT
+GTCTCTTAGGGAAAGCAGGAGCCTCTCTGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTT
+TTCCCAGAGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAG
+CTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGGTGGAGAAGGGGTGAA
+GGGTGGGGTCTGAGATTTCTTGTCTCACTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATT
+ACTGGGAAGCACCTTCCACAATCATGGGCCGACCCAGCCTGGGCCCTGTGTGCCAGCACTTACTCTTTTG
+TAAAGCACCTGTTAAAATGAAGGACAGATTTATCACCTTGATTACGGCGGTGATGGGACCTGATCCCAGC
+AGTCACAAGTCACAGGGGAAGGTCCCTGAGGACAGACCTCAGGAGGGCTATTGGTCCAGGACCCACACCT
+GCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCC
+AAGACTAGGAGGTTCCTCTAGGACCTTAAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTC
+CCACAGATAGAAAAGGAGGGAGTTACACTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTC
+CTTGGGATATTGTGTTTGGGAGCCCATGGGGGAGCTCACCCACCCCACAATTCCTCCTCTAGCCACATCT
+TCTGTGGGATCTGACCAGGTTCTGTTTTTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTG
+TCTCTCACAGCTTGTAAAGGTGAGAGCTTGGAGGGCCTGATGTGTGTTGGGTGTTGGGTGGAACAGTGGA
+CACAGCTGTGCTATGGGGTTTCTTTGCGTTGGATGTATTGAGCATGCGATGGGCTGTTTAAGGTGTGACC
+CCTCACTGTGATGGATATGAATTTGTTCATGAATATTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTG
+GGACTGAGAGGCAAGAGTTGTTCCTGCCCTTCCCTTTGTGACTTGAAGAACCCTGACTTTGTTTCTGCAA
+AGGCACCTGCATGTGTCTGTGTTCGTGTAGGCATAATGTGAGGAGGTGGGGAGAGCACCCCACCCCCATG
+TCCACCATGACCCTCTTCCCACGCTGACCTGTGCTCCCTCTCCAATCATCTTTCCTGTTCCAGAGAGGTG
+GGGCTGAGGTGTCTCCATCTCTGTCTCAACTTCATGGTGCACTGAGCTGTAACTTCTTCCTTCCCTATTA
+AAA

bio/orthanq/hla/candidates/test/hla.xml

@@ -0,0 +1,127 @@
+<?xml version="1.0" encoding="ISO-8859-1" ?>
+<alleles xmlns="http://hla.alleles.org/xml" xmlns:xs="http://www.w3.org/2001/XMLSchema" xs:noNamespaceSchemaLocation="http://hla.alleles.org/xml/hla.xsd">
+  <allele id="HLA00001" name="HLA-A*01:01:01:01" dateassigned="1989-08-01">
+    <releaseversions firstreleased="1.0.0" lastupdated="1.0.0" currentrelease="3.55.0" releasestatus="Public" releasecomments="Sequence unchanged" confirmed="Confirmed"/>
+    <locus genesystem="HLA" locusname="HLA-A" hugogenename="HLA-A" class="I" />
+    <cwd_catalogue cwd_version="2.0.0" cwd_reference="http://doi.org/10.1111/tan.12093">
+       <cwd_entry population="Undefined" status="C" />
+    </cwd_catalogue>
+    <cwd_catalogue cwd_version="3.0.0" cwd_reference="http://doi.org/10.1111/tan.13811">
+       <cwd_entry population="AFA" status="C" />
+       <cwd_entry population="API" status="C" />
+       <cwd_entry population="EURO" status="C" />
+       <cwd_entry population="HIS" status="C" />
+       <cwd_entry population="MENA" status="C" />
+       <cwd_entry population="NAM" status="C" />
+       <cwd_entry population="Total" status="C" />
+       <cwd_entry population="UNK" status="C" />
+    </cwd_catalogue>
+    <hla_g_group status="A*01:01:01G"/>
+    <hla_p_group status="A*01:01P"/>
+    <citations>
+      <citation pubmed="3375250" authors="Parham P, Lomen CE, Lawlor DA, Ways JP, Holmes N, Coppin HL, Salter RD, Wan AM, Ennis PD" title="Nature of polymorphism in HLA-A, -B, and -C molecules." location="Proceedings of the National Academy of Sciences USA 85:4005-4009 (1988)." />
+      <citation pubmed="2251137" authors="Girdlestone J" title="Nucleotide sequence of an HLA-A1 gene." location="Nucleic Acids Research 18:6701 (1990)." />
+      <citation pubmed="9349617" authors="Laforet M, Froelich N, Parissiadis A, Pfeiffer B, Schell A, Faller B, Woehl-Jaegle ML, Cazenave JP, Tongio MM" title="A nucleotide insertion in exon 4 is responsible for the absence of expression of an HLA-A*01 allele." location="Tissue Antigens 50:347-350 (1997)." />
+      <citation pubmed="15140828" authors="Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM, Humphray SJ, Hunt S, Mungall AJ, Osoegawa K, Palmer S, Roberts AN, Rogers J, Sims S, Wang Y, Wilming LG, Elliott JF, de Jong PJ, Sawcer S, Todd JA, Trowsdale J, Beck S" title="Complete MHC haplotype sequencing for common disease gene mapping." location="Genome Research 14:1176-1187 (2004)." />
+      <citation pubmed="18193213" authors="Horton R, Gibson R, Coggill P, Miretti M, Allcok RJ, Almeida J, Forbes S, Gilbert JGR, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S" title="Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project." location="Immunogenetics 60:1-18 (2008)." />
+      <citation pubmed="19735485" authors="Zhu F, He Y, Zhang W, He J, He J, Xu X, Yan L" title="Analysis of the complete genomic sequence of HLA-A alleles in the Chinese Han population." location="International Journal of Immunogenetics 36:351-360 (2009)." />
+      <citation pubmed="24673518" authors="Lu L, Xu YP" title="Genomic full-length sequence of two HLA-A alleles, A*01:01:01:01 and A*01:03, identified by cloning and sequencing." location="Tissue Antigens 83:423-424 (2014)." />
+    </citations>
+    <sourcexrefs>
+      <xref acc="AJ278305" pid="CAB93537.1" />
+      <xref acc="AL645935" />
+      <xref acc="CR759913" pid="CAQ08202.1" />
+      <xref acc="EU445470" pid="ACA34990.1" />
+      <xref acc="GU812295" pid="ADE80886.1" />
+      <xref acc="HG794373" pid="CDK41182.1" />
+      <xref acc="M24043" pid="AAA59652.1" />
+      <xref acc="OR126295" pid="WMP24209.1" />
+      <xref acc="X55710" pid="CAA39243.1" />
+      <xref acc="Z93949" pid="CAB07989.1" />
+    </sourcexrefs>
+    <sourcematerial>
+      <species latinname="Homo sapiens" commonname="Human" ncbitaxon="9606" />
+      <ancestry>
+        <sample_ancestry>Asian - East Asian</sample_ancestry>
+        <sample_ancestry>European</sample_ancestry>
+        <sample_ancestry>Undefined</sample_ancestry>
+      </ancestry>
+      <samples>
+        <sample name="7550800303" />
+        <sample name="APD" />
+        <sample name="B4702" />
+        <sample name="COX" />
+        <sample name="DE-SMS_A-575369" />
+        <sample name="LCL721" />
+        <sample name="MOLT-4" />
+        <sample name="PP" />
+      </samples>
+    </sourcematerial>
+    <sequence>
+      <alignmentreference allelename="A*01:01:01:01" alleleid="HLA00001" />
+      <nucsequence>CAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTACGTAGGGTCCTTCATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGAGGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACTCCGAGACCCTTGTCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCGGTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTATAGATCTCCCGGGCTGGCCTCCCACAAGGAGGGGAGACAATTGGGACCAACACTAGAATATCACCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGGTTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAATCTCTGAAGGAGTGACGGGAAGACGATCCCTCGAATACTGATGAGTGGTTCCCTTTGACACCGGCAGCAGCCTTGGGCCCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTTCACACTCAATGTGTGTGGGGGTCTGAGTCCAGCACTTCTGAGTCTCTCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCCTTCTCAGGGAATAGAAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGTGTCCTGTCCATTCTCAAGATGGCCACATGCGTGCTGGTGGAGTGTCCCATGACAGATGCAAAATGCCTGAATTTTCTGACTCTTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGGGTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCAGGAGCCTCTCTGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAGAGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCACTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCTTCCACAATCATGGGCCGACCCAGCCTGGGCCCTGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTTAAAATGAAGGACAGATTTATCACCTTGATTACGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCTGAGGACAGACCTCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCCCACAGATAGAAAAGGAGGGAGTTACACTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGTTTGGGAGCCCATGGGGGAGCTCACCCACCCCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGACCAGGTTCTGTTTTTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGTAAAGGTGAGAGCTTGGAGGGCCTGATGTGTGTTGGGTGTTGGGTGGAACAGTGGACACAGCTGTGCTATGGGGTTTCTTTGCGTTGGATGTATTGAGCATGCGATGGGCTGTTTAAGGTGTGACCCCTCACTGTGATGGATATGAATTTGTTCATGAATATTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAGAGGCAAGAGTTGTTCCTGCCCTTCCCTTTGTGACTTGAAGAACCCTGACTTTGTTTCTGCAAAGGCACCTGCATGTGTCTGTGTTCGTGTAGGCATAATGTGAGGAGGTGGGGAGAGCACCCCACCCCCATGTCCACCATGACCCTCTTCCCACGCTGACCTGTGCTCCCTCTCCAATCATCTTTCCTGTTCCAGAGAGGTGGGGCTGAGGTGTCTCCATCTCTGTCTCAACTTCATGGTGCACTGAGCTGTAACTTCTTCCTTCCCTATTAAAA</nucsequence>
+      <feature id="1.1" order="1" featuretype="UTR" name="5' UTR">
+        <SequenceCoordinates start="1" end="300" />
+      </feature>
+      <feature id="1.2" order="2" featuretype="Exon" name="Exon 1" status="Complete" >
+        <SequenceCoordinates start="301" end="373" />
+        <cDNACoordinates start="1" end="73"  readingframe="1" />
+      </feature>
+      <feature id="1.3" order="3" featuretype="Intron" name="Intron 1">
+        <SequenceCoordinates start="374" end="503" />
+      </feature>
+      <feature id="1.4" order="4" featuretype="Exon" name="Exon 2" status="Complete" >
+        <SequenceCoordinates start="504" end="773" />
+        <cDNACoordinates start="74" end="343"  readingframe="3" />
+      </feature>
+      <feature id="1.5" order="5" featuretype="Intron" name="Intron 2">
+        <SequenceCoordinates start="774" end="1014" />
+      </feature>
+      <feature id="1.6" order="6" featuretype="Exon" name="Exon 3" status="Complete" >
+        <SequenceCoordinates start="1015" end="1290" />
+        <cDNACoordinates start="344" end="619"  readingframe="3" />
+      </feature>
+      <feature id="1.7" order="7" featuretype="Intron" name="Intron 3">
+        <SequenceCoordinates start="1291" end="1869" />
+      </feature>
+      <feature id="1.8" order="8" featuretype="Exon" name="Exon 4" status="Complete" >
+        <SequenceCoordinates start="1870" end="2145" />
+        <cDNACoordinates start="620" end="895"  readingframe="3" />
+      </feature>
+      <feature id="1.9" order="9" featuretype="Intron" name="Intron 4">
+        <SequenceCoordinates start="2146" end="2247" />
+      </feature>
+      <feature id="1.10" order="10" featuretype="Exon" name="Exon 5" status="Complete" >
+        <SequenceCoordinates start="2248" end="2364" />
+        <cDNACoordinates start="896" end="1012"  readingframe="3" />
+      </feature>
+      <feature id="1.11" order="11" featuretype="Intron" name="Intron 5">
+        <SequenceCoordinates start="2365" end="2806" />
+      </feature>
+      <feature id="1.12" order="12" featuretype="Exon" name="Exon 6" status="Complete" >
+        <SequenceCoordinates start="2807" end="2839" />
+        <cDNACoordinates start="1013" end="1045"  readingframe="3" />
+      </feature>
+      <feature id="1.13" order="13" featuretype="Intron" name="Intron 6">
+        <SequenceCoordinates start="2840" end="2981" />
+      </feature>
+      <feature id="1.14" order="14" featuretype="Exon" name="Exon 7" status="Complete" >
+        <SequenceCoordinates start="2982" end="3029" />
+        <cDNACoordinates start="1046" end="1093"  readingframe="3" />
+      </feature>
+      <feature id="1.15" order="15" featuretype="Intron" name="Intron 7">
+        <SequenceCoordinates start="3030" end="3198" />
+      </feature>
+      <feature id="1.16" order="16" featuretype="Exon" name="Exon 8" status="Complete" >
+        <SequenceCoordinates start="3199" end="3203" />
+        <cDNACoordinates start="1094" end="1098"  readingframe="3" />
+      </feature>
+      <feature id="1.17" order="17" featuretype="UTR" name="3' UTR">
+        <SequenceCoordinates start="3204" end="3503" />
+      </feature>
+      <feature id="1.18" name="Translation" featuretype="Protein">
+        <translation>MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSLTACKV</translation>
+      </feature>
+    </sequence>
+  </allele>
+</alleles>

bio/orthanq/hla/candidates/test/hla_alleles.fasta

@@ -0,0 +1,9 @@
+>HLA:HLA00001 A*01:01:01:01 3503 bp
+CAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAG
+GCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAG
+TTTCTTTTCTCCCTCTCCCAACCTACGTAGGGTCCTTCATCCTGGATACTCACGACGCGG
+ACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCG
+GTCGCTGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGG
+ATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACC
+CAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAG
+GGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGAGGAGGGTCGGGCAGG

bio/orthanq/hla/candidates/wrapper.py

@@ -0,0 +1,13 @@
+__author__ = "Hamdiye Uzuner"
+__copyright__ = "Copyright 2024, Hamdiye Uzuner"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+shell(
+    "orthanq candidates hla --allele-freq {snakemake.input.allele_freq} "
+    " --alleles {snakemake.input.alleles} --genome {snakemake.input.genome} "
+    " --xml {snakemake.input.xml} --output {snakemake.output[0]} {log}"
+)

bio/orthanq/virus/candidates/environment.yaml

@@ -0,0 +1,2 @@
+dependencies:
+  - orthanq =1.1.0

bio/orthanq/virus/candidates/meta.yaml

@@ -0,0 +1,6 @@
+name: orthanq candidates virus
+description: |
+  Orthanq candidates virus subcommand generates candidate variants required for viral lineage quantification.
+url: https://github.com/orthanq/orthanq
+authors:
+  - Hamdiye Uzuner

bio/orthanq/virus/candidates/test/Snakefile

@@ -0,0 +1,7 @@
+rule orthanq_candidates_virus:
+    output:
+        directory("viral_candidates"),
+    log:
+        "logs/orthanq_candidates/candidates_virus.log",
+    wrapper:
+        "master/bio/orthanq/virus/candidates"

bio/orthanq/virus/candidates/wrapper.py

@@ -0,0 +1,11 @@
+__author__ = "Hamdiye Uzuner"
+__copyright__ = "Copyright 2024, Hamdiye Uzuner"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+shell(
+    "orthanq candidates virus --output {snakemake.output[0]} {log}"
+)