Merge pull request #158 from Clinical-Genomics/rename-files (minor)

New gms-artic version and change name of files for nanopore analyses

Author: henningonsbring

mutant/cli.py

@@ -12,9 +12,9 @@
 from mutant.modules.artic_illumina.start import RunSC2
 from mutant.modules.artic_nanopore.reformat import reformat_fastq_folder
 from mutant.modules.artic_nanopore.report import ReportPrinterNanopore
+from mutant.modules.delivery import DeliverySC2
 from mutant.modules.generic_parser import get_json
 from mutant.modules.artic_illumina.report import ReportSC2
-from mutant.modules.artic_illumina.delivery import DeliverySC2
 
 
 @click.group()
@@ -90,6 +90,7 @@ def sarscov2(
         WD=WD,
     )
 
+    barcode_to_sampleid = {}
     resdir = run.get_results_dir(config_mutant, outdir)
     if nanopore:
         barcode_to_sampleid: dict = reformat_fastq_folder(
@@ -119,14 +120,17 @@ def sarscov2(
             )
             report.create_all_files()
 
-        # Deliverables
-        if config_case != "":
-            delivery = DeliverySC2(
-                caseinfo=config_case,
-                indir=os.path.abspath(resdir),
-            )
+    # Deliverables
+    if config_case != "":
+        delivery = DeliverySC2(
+            caseinfo=config_case,
+            indir=os.path.abspath(resdir),
+            nanopore=nanopore,
+            timestamp=TIMESTAMP,
+            barcode_to_sampleid=barcode_to_sampleid,
+        )
 
-            delivery.rename_deliverables()
+        delivery.rename_deliverables()
 
 
 @analyse.command()

mutant/externals/gms-artic

@@ -139,11 +139,11 @@ def get_pangolin_type(raw_pangolin_result: str) -> str:
     return lineage
 
 
-def get_pangoLEARN_version(raw_pangolin_result: str) -> str:
-    """Return the pangoLEARN_version of a sample"""
+def get_pango_version(raw_pangolin_result: str) -> str:
+    """Return version of the lineage predictor used in pangolin"""
     split_on_comma = raw_pangolin_result.split(",")
-    pango_learn_version = split_on_comma[9]
-    return pango_learn_version
+    pango_version = split_on_comma[8]
+    return pango_version
 
 
 def identify_classifications() -> dict:
@@ -166,10 +166,10 @@ def parse_pangolin(results: dict, barcode_to_sampleid: dict, resdir: str) -> dic
         )
         pangolin_type: str = get_pangolin_type(raw_pangolin_result=second_line)
         results[cust_sample_id]["pangolin_type"] = pangolin_type
-        pangoLEARN_version: str = get_pangoLEARN_version(
+        pango_version: str = get_pango_version(
             raw_pangolin_result=second_line
         )
-        results[cust_sample_id]["pangolearn_version"] = pangoLEARN_version
+        results[cust_sample_id]["pangolin_data_version"] = pango_version
         voc_strains: dict = identify_classifications()
         if pangolin_type in voc_strains["lineage"]:
             index = voc_strains["lineage"].index(pangolin_type)

mutant/modules/artic_illumina/delivery.py

@@ -1,7 +1,9 @@
 """ Using a dict as input, this class will print a report covering the
     information requested by the sarscov2-customers at Clinical Genomics
 """
+import csv
 import glob
+import os
 from datetime import date
 
 from mutant.modules.artic_nanopore.parser import collect_results, collect_variants
@@ -55,8 +57,32 @@ def create_all_nanopore_files(self):
             target_files=self.consensus_target_files
         )
         generic_reporter.create_deliveryfile(fastq_dir=self.fastq_dir)
-        # TODO rename_vcfs
-        # TODO handle consensus files
+        self.create_fohm_csv(result=result)
+        self.create_instrument_properties()
+
+    def create_instrument_properties(self) -> None:
+        """Creates a properties file with instrument information"""
+        propfile = os.path.join(self.indir, "instrument.properties")
+        with open(propfile, "w") as prop:
+            prop.write("instrument=GridION\n")
+            prop.write("plattform=Oxford Nanopore Technologies\n")
+            prop.write("biblioteksmetod=NA:NA - None\n")
+            prop.write("lanes=1\n")
+
+    def create_fohm_csv(self, result: dict) -> None:
+        """Creates a summary file for FoHMs additional info"""
+        sumfile = os.path.join(
+            self.indir,
+            "{}_komplettering.csv".format(self.ticket),
+        )
+        with open(sumfile, "w") as out:
+            summary = csv.writer(out)
+            summary.writerow(["provnummer", "urvalskriterium", "GISAID_accession"])
+            samples = result.keys()
+            for sample in samples:
+                if result[sample]["qc_pass"] != "TRUE":
+                    continue
+                summary.writerow([sample, result[sample]["selection_criteria"]])
 
     def print_variants(self, variants: list) -> None:
         """Append data to the variant report"""
@@ -91,7 +117,7 @@ def print_report(self, result: dict) -> None:
                     "%10X_coverage",
                     "QC_pass",
                     "Lineage",
-                    "PangoLEARN_version",
+                    "Pangolin_data_version",
                     "VOC",
                     "Mutations\n",
                 ]
@@ -109,7 +135,7 @@ def print_report(self, result: dict) -> None:
                         result[sample]["pct_10x_coverage"],
                         result[sample]["qc_pass"],
                         result[sample]["pangolin_type"],
-                        result[sample]["pangolearn_version"],
+                        result[sample]["pangolin_data_version"],
                         result[sample]["voc"],
                         result[sample]["mutations"],
                         "\n",