Release 0.4.2 (#3)

Release 0.4.2

Dockerfile

@@ -14,7 +14,6 @@ RUN mkdir /docs/
 
 COPY moalmanac/test/ moalmanac/test/
 COPY moalmanac/datasources/acmg/ /moalmanac/datasources/acmg/
-COPY moalmanac/datasources/moalmanac/ /moalmanac/datasources/moalmanac/
 COPY moalmanac/datasources/cancergenecensus/ /moalmanac/datasources/cancergenecensus/
 COPY moalmanac/datasources/cancerhotspots/ /moalmanac/datasources/cancerhotspots/
 COPY moalmanac/datasources/clinvar/ /moalmanac/datasources/clinvar/
@@ -25,20 +24,24 @@ COPY moalmanac/datasources/hereditary/ /moalmanac/datasources/hereditary/
 COPY moalmanac/datasources/lawrence/ /moalmanac/datasources/lawrence/
 COPY moalmanac/datasources/oncotree/ /moalmanac/datasources/oncotree/
 
-COPY moalmanac/datasources/preclinical/almanac-gdsc-mappings.json /moalmanac/datasources/preclinical/almanac-gdsc-mappings.json
-COPY moalmanac/datasources/preclinical/cell-lines.summary.txt /moalmanac/datasources/preclinical/cell-lines.summary.txt
-COPY moalmanac/datasources/preclinical/ccle.variants.evaluated.txt /moalmanac/datasources/preclinical/ccle.variants.evaluated.txt
-COPY moalmanac/datasources/preclinical/ccle.copy-numbers.evaluated.txt /moalmanac/datasources/preclinical/ccle.copy-numbers.evaluated.txt
-COPY moalmanac/datasources/preclinical/sanger.fusions.evaluated.txt /moalmanac/datasources/preclinical/sanger.fusions.evaluated.txt
-COPY moalmanac/datasources/preclinical/sanger.fusions.gene1.evaluated.txt /moalmanac/datasources/preclinical/sanger.fusions.gene1.evaluated.txt
-COPY moalmanac/datasources/preclinical/sanger.fusions.gene2.evaluated.txt /moalmanac/datasources/preclinical/sanger.fusions.gene2.evaluated.txt
-COPY moalmanac/datasources/preclinical/sanger.gdsc.txt /moalmanac/datasources/preclinical/sanger.gdsc.txt
-COPY moalmanac/datasources/preclinical/cell-lines.pkl /moalmanac/datasources/preclinical/cell-lines.pkl
-
 COPY moalmanac/templates/ /moalmanac/templates/
 COPY moalmanac/wrapper_deconstructsigs.sh moalmanac/run_deconstructsigs.R /moalmanac/
 COPY moalmanac/*.py moalmanac/*.ini /moalmanac/
 
+COPY moalmanac/datasources/moalmanac/ /moalmanac/datasources/moalmanac/
+
+COPY moalmanac/datasources/preclinical/README.md /moalmanac/datasources/preclinical/README.md
+COPY moalmanac/datasources/preclinical/generate-dictionary.ipynb /moalmanac/datasources/preclinical/generate-dictionary.ipynb
+COPY moalmanac/datasources/preclinical/cell-lines.pkl /moalmanac/datasources/preclinical/cell-lines.pkl
+COPY moalmanac/datasources/preclinical/formatted/almanac-gdsc-mappings.json /moalmanac/datasources/preclinical/formatted/almanac-gdsc-mappings.json
+COPY moalmanac/datasources/preclinical/formatted/cell-lines.summary.txt /moalmanac/datasources/preclinical/formatted/cell-lines.summary.txt
+COPY moalmanac/datasources/preclinical/annotated/cell-lines.somatic-variants.annotated.txt /moalmanac/datasources/preclinical/annotated/cell-lines.somatic-variants.annotated.txt
+COPY moalmanac/datasources/preclinical/annotated/cell-lines.copy-numbers.annotated.txt  /moalmanac/datasources/preclinical/annotated/cell-lines.copy-numbers.annotated.txt
+COPY moalmanac/datasources/preclinical/annotated/cell-lines.fusions.annotated.txt  /moalmanac/datasources/preclinical/annotated/cell-lines.fusions.annotated.txt
+COPY moalmanac/datasources/preclinical/annotated/cell-lines.fusions.annotated.gene1.txt /moalmanac/datasources/preclinical/annotated/cell-lines.fusions.annotated.gene1.txt
+COPY moalmanac/datasources/preclinical/annotated/cell-lines.fusions.annotated.gene2.txt /moalmanac/datasources/preclinical/annotated/cell-lines.fusions.annotated.gene2.txt
+COPY moalmanac/datasources/preclinical/formatted/sanger.gdsc.txt /moalmanac/datasources/preclinical/formatted/sanger.gdsc.txt
+
 COPY docs/* /docs/
 COPY README.md /
 COPY LICENSE /

moalmanac/annotator.py

@@ -960,7 +960,7 @@ def append_exac_af(cls, df, ds, ds_columns):
         #ds = ds.loc[:, [cls.chr, cls.start, cls.ref, cls.alt, cls.af]]
         ds = ds.loc[:, ds_columns]
 
-        for column, data_type in [(cls.str_columns, str), (cls.int_columns, int)]:
+        for column, data_type in [(cls.str_columns, str), (cls.int_columns, float), (cls.int_columns, int)]:
             variants.loc[variants.index, column] = cls.format_columns(variants, column, data_type)
             ds.loc[ds.index, column] = cls.format_columns(ds, column, data_type)
 

moalmanac/colnames.ini

@@ -607,6 +607,7 @@ sensitive_implication_map = ${maps:sensitive_implication_map}
 sensitive_therapy = ${maps:sensitive_therapy}
 sensitive_therapy_type = ${maps:sensitive_therapy_type}
 sensitive_therapy_strategy = ${maps:sensitive_therapy_strategy}
+sensitive_oncotree_code = ${maps:sensitive_oncotree_code}
 sensitive_description = ${maps:sensitive_description}
 sensitive_url = ${maps:sensitive_url}
 sensitive_citation = ${maps:sensitive_citation}
@@ -615,12 +616,14 @@ resistance_implication_map = ${maps:resistance_implication_map}
 resistance_therapy = ${maps:resistance_therapy}
 resistance_therapy_type = ${maps:resistance_therapy_type}
 resistance_therapy_strategy = ${maps:resistance_therapy_strategy}
+resistance_oncotree_code = ${maps:resistance_oncotree_code}
 resistance_description = ${maps:resistance_description}
 resistance_url = ${maps:resistance_url}
 resistance_citation = ${maps:resistance_citation}
 prognostic_implication = ${maps:prognostic_implication}
 prognostic_implication_map = ${maps:prognostic_implication_map}
 favorable_prognosis = ${maps:prognosis}
+prognostic_oncotree_code = ${maps:prognostic_oncotree_code}
 prognostic_description = ${maps:prognostic_description}
 prognostic_url = ${maps:prognostic_url}
 prognostic_citation = ${maps:prognostic_citation}

moalmanac/config.ini

@@ -1,5 +1,5 @@
 [versions]
-interpreter = 0.4.1
+interpreter = 0.4.2
 database = v.2021-02-04
 
 [exac]

moalmanac/writer.py

@@ -33,6 +33,9 @@ class Writer(object):
     sensitive_therapy_type = COLNAMES[section]['sensitive_therapy_type']
     resistance_therapy_type = COLNAMES[section]['resistance_therapy_type']
     favorable_prognosis = COLNAMES[section]['favorable_prognosis']
+    sensitive_oncotree_code = COLNAMES[section]['sensitive_oncotree_code']
+    resistance_oncotree_code = COLNAMES[section]['resistance_oncotree_code']
+    prognostic_oncotree_code = COLNAMES[section]['prognostic_oncotree_code']
     sensitive_description = COLNAMES[section]['sensitive_description']
     resistance_description = COLNAMES[section]['resistance_description']
     prognostic_description = COLNAMES[section]['prognostic_description']
@@ -130,11 +133,14 @@ class Actionable(object):
                       Writer.tumor_f, Writer.coverage, Writer.exac_af, Writer.exac_common, Writer.clinvar,
                       Writer.sensitive_bin,
                       Writer.sensitive_therapy, Writer.sensitive_therapy_strategy, Writer.sensitive_therapy_type,
+                      Writer.sensitive_oncotree_code,
                       Writer.sensitive_description, Writer.sensitive_citation, Writer.sensitive_url,
                       Writer.resistance_bin,
                       Writer.resistance_therapy, Writer.resistance_therapy_strategy, Writer.resistance_therapy_type,
+                      Writer.resistance_oncotree_code,
                       Writer.resistance_description, Writer.resistance_citation, Writer.resistance_url,
                       Writer.prognostic_bin, Writer.favorable_prognosis,
+                      Writer.prognostic_oncotree_code,
                       Writer.prognostic_description, Writer.prognostic_citation, Writer.prognostic_url,
                       Writer.number_germline_mutations,
                       Writer.validation_coverage, Writer.validation_tumor_f, Writer.validation_detection_power,

terra/almanac.wdl

@@ -16,11 +16,11 @@ workflow MolecularOncologyAlmanac {
     String? whole_genome_doubling
     String? disable_matchmaking
 
-    Int? RAM = 6
-    Int? SSD = 25
+    Int? RAM = 8
+    Int? SSD = 50
     Int? preemptible = 3
 
-    String? docker_tag = "0.4.1_v.2021-02-04"
+    String? docker_tag = "0.4.2_v.2021-02-04"
 
     meta {
         author: "Brendan Reardon"
@@ -117,7 +117,7 @@ task almanacTask {
         mkdir docs
         cp -r /docs/* docs/
 
-        tar -zcf ${patientId}.almanac.tar.gz ${patientId}* docs
+        tar -zcf ${patientId}.almanac.tar.gz ${patientId}* docs almanac.additional.matches.json
     }
 
     output  {