more nextstrain edits

notes.md

@@ -83,12 +83,28 @@ NucleotidePseudoGenesTotal
 NucleotiderRNAs
 AssemblySubmissionDate
 SRARunPublishDate
+BioSampleComment
+
+```
+# General
+./sqlite_NextStrain_tsv.py   --database ../results/ncbimeta_db/update/latest/output/database/yersinia_pestis_db.sqlite   --query "SELECT BioSampleAccession,AssemblyFTPGenbank,SRARunAccession,BioSampleStrain,BioSampleCollectionDate,BioSampleHost,BioSampleGeographicLocation,BioSampleBiovar,PubmedArticleTitle,PubmedAuthorsLastName,AssemblyContigCount,AssemblyTotalLength,NucleotideGenes,NucleotideGenesTotal,NucleotidePseudoGenes,NucleotidePseudoGenesTotal,NucleotiderRNAs,AssemblySubmissionDate,SRARunPublishDate,BioSampleComment FROM Master"   --output metadata_all_nextstrain.tsv
+
+
+# Both Assembly and SRA
+SELECT BioSampleAccession,AssemblyFTPGenbank,SRARunAccession,BioSampleStrain,BioSampleCollectionDate,BioSampleHost,BioSampleGeographicLocation,BioSampleBiovar,PubmedArticleTitle,PubmedAuthorsLastName,AssemblyContigCount,AssemblyTotalLength,NucleotideGenes,NucleotideGenesTotal,NucleotidePseudoGenes,NucleotidePseudoGenesTotal,NucleotiderRNAs,AssemblySubmissionDate,SRARunPublishDate,BioSampleComment FROM Master WHERE BioSampleComment NOT LIKE '%REMOVE%'
+
+# Only Assembly
+./sqlite_NextStrain_tsv.py   --database ../results/ncbimeta_db/update/latest/output/database/yersinia_pestis_db.sqlite   --query "SELECT BioSampleAccession,AssemblyFTPGenbank,SRARunAccession,BioSampleStrain,BioSampleCollectionDate,BioSampleHost,BioSampleGeographicLocation,BioSampleBiovar,PubmedArticleTitle,PubmedAuthorsLastName,AssemblyContigCount,AssemblyTotalLength,NucleotideGenes,NucleotideGenesTotal,NucleotidePseudoGenes,NucleotidePseudoGenesTotal,NucleotiderRNAs,AssemblySubmissionDate,SRARunPublishDate,BioSampleComment FROM Master WHERE (BioSampleComment NOT LIKE '%REMOVE%' AND TRIM(AssemblyFTPGenbank) > '')"   --output metadata_assembly_nextstrain.tsv
+
+We need to add the mandatory column sample/name
+```
+
 
-SELECT BioSampleAccession,AssemblyFTPGenbank,SRARunAccession,BioSampleStrain,BioSampleCollectionDate,BioSampleHost,BioSampleGeographicLocation,BioSampleBiovar,PubmedArticleTitle,PubmedAuthorsLastName,AssemblyContigCount,AssemblyTotalLength,NucleotideGenes,NucleotideGenesTotal,NucleotidePseudoGenes,NucleotidePseudoGenesTotal,NucleotiderRNAs,AssemblySubmissionDate,SRARunPublishDate FROM Master WHERE BioSampleComment NOT LIKE '%REMOVE%'
 
 ## NCBI Filtering by Attribute AHA!!!
 ```
 "geo_loc_name=Russia: Chechnya"[attr]
+"project_name=Rise of the Bronze Age"[attr]
 ```
 
 ## NextStrain setup

scripts/sqlite_NextStrain_tsv.py

@@ -48,19 +48,13 @@
                     dest = 'outPath',
                     required = True)
 
-parser.add_argument('--split-col',
-                    help = 'Names of the column to check for splitting records (CSV).',
-                    action = 'store',
-                    dest = 'splitCol',
-                    required = False)
 
 # Retrieve user parameters
 args = vars(parser.parse_args())
 
 db_path = args['dbPath']
 sql_query = args['sqlQuery']
 out_path = args['outPath']
-split_col = args['splitCol']
 
 #------------------------------------------------------------------------------#
 #                            Error Catching                                    #