adjust read number in PE, version 1.0

yyoshiaki · Aug 10, 2020 · 7a83c5b · 7a83c5b
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Showing 17 changed files with 91 additions and 23 deletions.
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# VIRTUS : VIRal Transcript Usage Sensor v0.11 <img src="img/VIRTUS.jpg" width="20%" align="right" />
+# VIRTUS : VIRal Transcript Usage Sensor v1.0 <img src="img/VIRTUS.jpg" width="20%" align="right" />
 
 Virus transcript detection and quantification using normal human RNAseq. VIRTUS is the first tool to detect viral transcripts considering their splicing event rather than the viral genome copy number. VIRTUS can be applied to both bulk RNAseq and single-cell RNAseq. The virus reference covers 763 viruses including SARS-CoV-2 (cause of COVID-19). The workflow is implemented by [Common Workflow Language](https://www.commonwl.org/) and [Rabix](https://rabix.io/). You can specify each parameter individually or give `yaml` or `json` file which describes all the parameter information. In detail, check [the CWL User Guide](http://www.commonwl.org/user_guide/) out. 
 

diff --git a/tool/mk_summary_virus_count/humanLog.final.out b/tool/mk_summary_virus_count/humanLog.final.out
@@ -0,0 +1,37 @@
+                                 Started job on |	Feb 25 08:11:28
+                             Started mapping on |	Feb 25 08:12:02
+                                    Finished on |	Feb 25 08:46:51
+       Mapping speed, Million of reads per hour |	218.99
+
+                          Number of input reads |	127074247
+                      Average input read length |	200
+                                    UNIQUE READS:
+                   Uniquely mapped reads number |	46789415
+                        Uniquely mapped reads % |	36.82%
+                          Average mapped length |	196.83
+                       Number of splices: Total |	16249222
+            Number of splices: Annotated (sjdb) |	0
+                       Number of splices: GT/AG |	15726296
+                       Number of splices: GC/AG |	127630
+                       Number of splices: AT/AC |	8313
+               Number of splices: Non-canonical |	386983
+                      Mismatch rate per base, % |	0.35%
+                         Deletion rate per base |	0.01%
+                        Deletion average length |	1.91
+                        Insertion rate per base |	0.01%
+                       Insertion average length |	1.62
+                             MULTI-MAPPING READS:
+        Number of reads mapped to multiple loci |	68574496
+             % of reads mapped to multiple loci |	53.96%
+        Number of reads mapped to too many loci |	1040077
+             % of reads mapped to too many loci |	0.82%
+                                  UNMAPPED READS:
+  Number of reads unmapped: too many mismatches |	0
+       % of reads unmapped: too many mismatches |	0.00%
+            Number of reads unmapped: too short |	10608694
+                 % of reads unmapped: too short |	8.35%
+                Number of reads unmapped: other |	61565
+                     % of reads unmapped: other |	0.05%
+                                  CHIMERIC READS:
+                       Number of chimeric reads |	0
+                            % of chimeric reads |	0.00%
diff --git a/tool/mk_summary_virus_count/mk_summary_virus_count.cwl b/tool/mk_summary_virus_count/mk_summary_virus_count.cwl
@@ -15,6 +15,10 @@ inputs:
     type: File
     inputBinding:
       position: 2
+  - id: input_layout
+    type: string
+    inputBinding:
+      position: 4
 outputs:
   - id: output
     type: File?
@@ -23,4 +27,4 @@ outputs:
 label: mk_summary_virus_count
 requirements:
   - class: DockerRequirement
-    dockerPull: yyasumizu/mk_summary_virus_count
+    dockerPull: yyasumizu/mk_summary_virus_count:latest
diff --git a/tool/mk_summary_virus_count/mk_summary_virus_count.job.yaml b/tool/mk_summary_virus_count/mk_summary_virus_count.job.yaml
@@ -1,8 +1,9 @@
 input_STARLog:
   class: File
   path: >-
-    /Users/yasumizuyoshiaki/bioinformatics/EB_Virtect/donor1_day1/virusLog.final.out
+    /home/yyasumizu/Programs/VIRTUS/tool/mk_summary_virus_count/humanLog.final.out
 input_virus_count:
   class: File
   path: >-
-    /Users/yasumizuyoshiaki/bioinformatics/EB_Virtect/donor1_day1/virus_counts.txt
+    /home/yyasumizu/Programs/VIRTUS/tool/mk_summary_virus_count/virus_counts.txt
+input_layout: PE
diff --git a/tool/mk_summary_virus_count/mk_summary_virus_count.py b/tool/mk_summary_virus_count/mk_summary_virus_count.py
@@ -6,18 +6,24 @@
 2020.03.08
 
 ex.
-python mk_summary_virus_count.py output/donor1_day1/humanLog.final.out output/donor1_day1/virus_counts.txt
+python mk_summary_virus_count.py \
+    output/donor1_day1/humanLog.final.out \
+    output/donor1_day1/virus_counts.txt \
+    PE
 '''
 
 input_STARLog = sys.argv[1]
 input_virus_count = sys.argv[2]
+input_layout = sys.argv[3]
 
 df_STARLog = pd.read_csv(input_STARLog, sep='\t', header=None, index_col=0)
 num_reads = int(df_STARLog.loc['                   Uniquely mapped reads number |', 1]) + \
             int(df_STARLog.loc['        Number of reads mapped to multiple loci |', 1])
 
 df_virus_count = pd.read_csv(input_virus_count, delim_whitespace=True)
 df_virus_count.columns = ['num_hit', 'virus']
+if input_layout == 'PE':
+    df_virus_count['num_hit'] = df_virus_count['num_hit'] / 2
 df_virus_count['rate_hit'] = df_virus_count['num_hit'] / num_reads
 df_virus_count = df_virus_count[['virus', 'num_hit', 'rate_hit']]
 df_virus_count = df_virus_count.sort_values(by='rate_hit', ascending=False)

diff --git a/tool/mk_summary_virus_count/virus.counts.final.tsv b/tool/mk_summary_virus_count/virus.counts.final.tsv
@@ -0,0 +1,14 @@
+virus	num_hit	rate_hit
+NC_007605.1_Human_herpesvirus_4_complete_wild_type_genome	83054.0	0.0007199305162253037
+NC_009823.1_Hepatitis_C_virus_genotype_2,_complete_genome	77433.0	0.0006712064399411701
+NC_004102.1_Hepatitis_C_virus_genotype_1,_complete_genome	48047.0	0.00041648206604229986
+NC_018382.1_Bat_hepevirus,_complete_genome	18969.0	0.0001644275045425601
+NC_009334.1_Human_herpesvirus_4,_complete_genome	16602.0	0.0001439098228907999
+NC_001672.1_Tick-borne_encephalitis_virus,_complete_genome	5169.0	4.480603990618869e-05
+NC_002645.1_Human_coronavirus_229E,_complete_genome	3029.0	2.6256044665476017e-05
+NC_001716.2_Human_herpesvirus_7,_complete_genome	2917.0	2.5285203793064888e-05
+NC_015521.1_Cutthroat_trout_virus,_complete_genome	1927.0	1.67036639387165e-05
+NC_009827.1_Hepatitis_C_virus_genotype_6,_complete_genome	1558.0	1.350508999300483e-05
+NC_022518.1_Human_endogenous_retrovirus_K113_complete_genome	1002.0	8.685558519249578e-06
+gi|12084981|lcl|HPV71REF.1|_Human_papillomavirus_71_(HPV71),_complete_genome	538.0	4.663503476403465e-06
+NC_003977.1_Hepatitis_B_virus,_complete_genome	243.0	2.1063779642491488e-06
diff --git a/tool/mk_summary_virus_count/virus_counts.txt b/tool/mk_summary_virus_count/virus_counts.txt
@@ -0,0 +1,14 @@
+23161329 *
+  10338 NC_001672.1_Tick-borne_encephalitis_virus,_complete_genome
+   5834 NC_001716.2_Human_herpesvirus_7,_complete_genome
+   6058 NC_002645.1_Human_coronavirus_229E,_complete_genome
+    486 NC_003977.1_Hepatitis_B_virus,_complete_genome
+  96094 NC_004102.1_Hepatitis_C_virus_genotype_1,_complete_genome
+ 166108 NC_007605.1_Human_herpesvirus_4_complete_wild_type_genome
+  33204 NC_009334.1_Human_herpesvirus_4,_complete_genome
+ 154866 NC_009823.1_Hepatitis_C_virus_genotype_2,_complete_genome
+   3116 NC_009827.1_Hepatitis_C_virus_genotype_6,_complete_genome
+   3854 NC_015521.1_Cutthroat_trout_virus,_complete_genome
+  37938 NC_018382.1_Bat_hepevirus,_complete_genome
+   2004 NC_022518.1_Human_endogenous_retrovirus_K113_complete_genome
+   1076 gi|12084981|lcl|HPV71REF.1|_Human_papillomavirus_71_(HPV71),_complete_genome
diff --git a/tool/star/star_index/star_index.cwl b/tool/star/star_index/star_index.cwl
@@ -57,9 +57,6 @@ requirements:
 hints:
   - class: DockerRequirement
     dockerPull: 'quay.io/biocontainers/star:2.7.1a--0'
-$schemas:
-  - 'https://schema.org/docs/schema_org_rdfa.html'
-  - 'http://edamontology.org/EDAM_1.18.owl'
 's:author':
   - class: 's:Person'
     's:email': 'mailto:inutano@gmail.com'

diff --git a/tool/star/star_mapping-pe/star_mapping-pe.cwl b/tool/star/star_mapping-pe/star_mapping-pe.cwl
@@ -172,9 +172,6 @@ requirements:
 hints:
   - class: DockerRequirement
     dockerPull: 'quay.io/biocontainers/star:2.7.1a--0'
-$schemas:
-  - 'https://schema.org/docs/schema_org_rdfa.html'
-  - 'http://edamontology.org/EDAM_1.18.owl'
 's:author':
   - class: 's:Person'
     's:email': 'mailto:inutano@gmail.com'

diff --git a/tool/star/star_mapping-se/star_mapping-se.cwl b/tool/star/star_mapping-se/star_mapping-se.cwl
@@ -166,9 +166,6 @@ requirements:
 hints:
   - class: DockerRequirement
     dockerPull: 'quay.io/biocontainers/star:2.7.1a--0'
-$schemas:
-  - 'https://schema.org/docs/schema_org_rdfa.html'
-  - 'http://edamontology.org/EDAM_1.18.owl'
 's:author':
   - class: 's:Person'
     's:email': 'mailto:inutano@gmail.com'

diff --git a/workflow/VIRTUS.PE.cwl b/workflow/VIRTUS.PE.cwl
@@ -3,7 +3,7 @@
 class: Workflow
 cwlVersion: v1.0
 id: VIRTUS.PE
-doc: VIRTUS v0.11
+doc: VIRTUS v1.0
 label: VIRTUS.PE
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
@@ -292,6 +292,8 @@ steps:
         source: star_mapping_pe_human/mappingstats
       - id: input_virus_count
         source: mk_virus_count/virus_count
+      - id: input_layout
+        default: PE
     out:
       - id: output
     run: ../tool/mk_summary_virus_count/mk_summary_virus_count.cwl

diff --git a/workflow/VIRTUS.PE.singlevirus.cwl b/workflow/VIRTUS.PE.singlevirus.cwl
@@ -5,7 +5,7 @@ cwlVersion: v1.0
 id: VIRTUS.PE.singlevirus
 doc: >-
   STAR mapping and salmon quantification for one specified virus. Prepare using
-  create_singlevirus.cwl beforehand. version 0.11
+  create_singlevirus.cwl beforehand. version 1.0
 label: VIRTUS.PE.singlevirus
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'

diff --git a/workflow/VIRTUS.SE.cwl b/workflow/VIRTUS.SE.cwl
@@ -3,7 +3,7 @@
 class: Workflow
 cwlVersion: v1.0
 id: VIRTUS.SE
-doc: VIRTUS v0.11
+doc: VIRTUS v1.0
 label: VIRTUS.SE
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
@@ -157,6 +157,8 @@ steps:
         source: star_mapping_se/mappingstats
       - id: input_virus_count
         source: mk_virus_count/virus_count
+      - id: input_layout
+        default: SE
     out:
       - id: output
     run: ../tool/mk_summary_virus_count/mk_summary_virus_count.cwl

diff --git a/workflow/VIRTUS.SE.singlevirus.cwl b/workflow/VIRTUS.SE.singlevirus.cwl
@@ -5,7 +5,7 @@ cwlVersion: v1.0
 id: VIRTUS.PE.singlevirus
 doc: >-
   STAR mapping and salmon quantification for one specified virus. Prepare using
-  create_singlevirus.cwl beforehand. VIRTUS version 0.11
+  create_singlevirus.cwl beforehand. VIRTUS version 1.0
 label: VIRTUS.PE.singlevirus
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'

diff --git a/workflow/createindex.cwl b/workflow/createindex.cwl
@@ -4,7 +4,7 @@ class: Workflow
 cwlVersion: v1.0
 id: createindex
 label: CreateIndex
-doc: VIRTUS v0.11
+doc: VIRTUS v1.0
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 inputs:

diff --git a/workflow/createindex_singlevirus.cwl b/workflow/createindex_singlevirus.cwl
@@ -4,7 +4,7 @@ class: Workflow
 cwlVersion: v1.0
 id: createindex_singlevirus
 label: createindex_singlevirus
-doc: VIRTUS v0.11
+doc: VIRTUS v1.0
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 inputs:

diff --git a/workflow/rnaseq-star_index/rnaseq-star_index.cwl b/workflow/rnaseq-star_index/rnaseq-star_index.cwl
@@ -85,9 +85,6 @@ steps:
     'sbg:x': -233
     'sbg:y': -35
 requirements: []
-$schemas:
-  - 'https://schema.org/docs/schema_org_rdfa.html'
-  - 'http://edamontology.org/EDAM_1.18.owl'
 's:author':
   - class: 's:Person'
     's:email': 'mailto:inutano@gmail.com'