Merge pull request #209 from Sage-Bionetworks/rename-bed-file

Rename bed file
Sage-Bionetworks · Oct 26, 2019 · c78c0d3 · c78c0d3
2 parents 301f907 + d84359b
commit c78c0d3
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/genie/consortium_to_public.py b/genie/consortium_to_public.py
@@ -45,7 +45,7 @@ def consortiumToPublic(syn, processingDate, genie_version, releaseId, databaseSy
     MUTATIONS_PATH = os.path.join(dbTostaging.GENIE_RELEASE_DIR,'data_mutations_extended_%s.txt' % genie_version)
     FUSIONS_PATH = os.path.join(dbTostaging.GENIE_RELEASE_DIR,'data_fusions_%s.txt' % genie_version)
     SEG_PATH = os.path.join(dbTostaging.GENIE_RELEASE_DIR,'genie_public_data_cna_hg19_%s.seg' % genie_version)
-    COMBINED_BED_PATH = os.path.join(dbTostaging.GENIE_RELEASE_DIR,'genie_combined_%s.bed' % genie_version)
+    COMBINED_BED_PATH = os.path.join(dbTostaging.GENIE_RELEASE_DIR,'genomic_information_%s.txt' % genie_version)
 
     if not os.path.exists(dbTostaging.GENIE_RELEASE_DIR):
         os.mkdir(dbTostaging.GENIE_RELEASE_DIR)
@@ -186,12 +186,12 @@ def consortiumToPublic(syn, processingDate, genie_version, releaseId, databaseSy
             # panelDf = panelDf[panelDf['SAMPLE_ID'].isin(publicReleaseSamples)]
             # panelDf.to_csv(DATA_GENE_PANEL_PATH,sep="\t",index=False)
             # storeFile(syn, DATA_GENE_PANEL_PATH, PUBLIC_RELEASE_PREVIEW, ANONYMIZE_CENTER_DF, genie_version, name="data_gene_matrix.txt")
-        elif entName == "genie_combined.bed":
+        elif entName == "genomic_information.txt":
             bed = syn.get(entId, followLink=True)
             bedDf = pd.read_csv(bed.path, sep="\t")
             bedDf = bedDf[bedDf.SEQ_ASSAY_ID.isin(allClin.SEQ_ASSAY_ID)]
             bedDf.to_csv(COMBINED_BED_PATH,sep="\t",index=False)
-            storeFile(syn, COMBINED_BED_PATH, PUBLIC_RELEASE_PREVIEW, ANONYMIZE_CENTER_DF, genie_version, name="genie_combined.bed")
+            storeFile(syn, COMBINED_BED_PATH, PUBLIC_RELEASE_PREVIEW, ANONYMIZE_CENTER_DF, genie_version, name="genomic_information.txt")
         elif entName in ["data_clinical_sample.txt", "data_clinical_patient.txt"] or entName.endswith(".html"):
             continue
         elif entName.startswith("data_gene_panel"):

diff --git a/genie/dashboardTemplate.Rmd b/genie/dashboardTemplate.Rmd
@@ -337,7 +337,7 @@ if (is.null(this_samples)) {
   this_patient <- this_samples
   this_patient <- this_patient[!duplicated(this_patient$PATIENT_ID),]
 }
-this_bed <- getFileDf("genie_combined.bed", releaseFiles)
+this_bed <- getFileDf("genomic_information.txt", releaseFiles)
 this_assays = as.character(unique(this_samples$SEQ_ASSAY_ID))
 this_mut <- getFileDf("data_mutations_extended.txt", releaseFiles)
 black_list_variants <- synTableQuery("select * from syn18459663",

diff --git a/genie/database_to_staging.py b/genie/database_to_staging.py
@@ -473,7 +473,7 @@ def stagingToCbio(
     SEG_PATH = os.path.join(
         GENIE_RELEASE_DIR, 'genie_private_data_cna_hg19_%s.seg' % genieVersion)
     COMBINED_BED_PATH = os.path.join(
-        GENIE_RELEASE_DIR, 'genie_combined_%s.bed' % genieVersion)
+        GENIE_RELEASE_DIR, 'genomic_information_%s.txt' % genieVersion)
     consortiumReleaseSynId = databaseSynIdMappingDf['Id'][
         databaseSynIdMappingDf['Database'] == "consortium"][0]
     variant_filtering_synId = databaseSynIdMappingDf['Id'][
@@ -1110,7 +1110,7 @@ def stagingToCbio(
         syn, COMBINED_BED_PATH,
         parent=consortiumReleaseSynId,
         genieVersion=genieVersion,
-        name="genie_combined.bed",
+        name="genomic_information.txt",
         staging=current_release_staging)
 
     return(genePanelEntities)

diff --git a/genie/maf.py b/genie/maf.py
@@ -76,10 +76,10 @@ def createFinalMaf(self, mafDf, filePath, maf=False):
                 mafset = mafDf.to_csv(sep="\t", index=False)
             else:
                 mafset = mafDf.to_csv(sep="\t", index=False, header=None)
-            write_or_append = "w" if maf else "a"
+            write_or_append = "wb" if maf else "ab"
             with open(filePath, write_or_append) as maffile:
                 mafSet = process_functions.removeStringFloat(mafset)
-                maffile.write(mafSet)
+                maffile.write(mafSet.encode("utf-8"))
 
     def storeProcessedMaf(
             self, filePath, mafSynId, centerMafSynId, isNarrow=False):