Small fixes in autoclean_sftp and bioinfo-doc. Reverted excel_generator.py

CHANGELOG.md

@@ -13,6 +13,7 @@ Code contributions to the hotfix:
 ### Template fixes and updates
 
 - Added blast_nt template to services.json
+- Included new user to sftp_user.json
 
 ### Modules
 
@@ -22,8 +23,14 @@ Code contributions to the hotfix:
 
 #### Fixes
 
+- Autoclean_sftp does not crash anymore. New argument from 'utils.prompt_yn_question()' in v2.0.0 was missing: 'dflt'
+- Bioinfo-doc now sends email correctly to multiple CCs
+
 #### Changed
 
+- excel_generator.py reverted to last state, now lineage tables are merged when argument -l is given
+- Adapted viralrecon_results lablog to new excel_generator.py argument
+
 #### Removed
 
 ### Requirements

bu_isciii/autoclean_sftp.py

@@ -68,7 +68,9 @@ class AutoremoveSftpService:
     def __init__(self, path=None, days=14):
         # Parse input path
         if path is None:
-            use_default = bu_isciii.utils.prompt_yn_question("Use default path?: ")
+            use_default = bu_isciii.utils.prompt_yn_question(
+                "Use default path?: ", dflt=False
+            )
             if use_default:
                 data_path = bu_isciii.config_json.ConfigJson().get_configuration(
                     "global"
@@ -149,7 +151,9 @@ def remove_oldservice(self):
                 "The following services are going to be deleted from the sftp:\n"
                 + service_elements
             )
-            confirm_sftp_delete = bu_isciii.utils.prompt_yn_question("Are you sure?: ")
+            confirm_sftp_delete = bu_isciii.utils.prompt_yn_question(
+                "Are you sure?: ", dflt=False
+            )
             if confirm_sftp_delete:
                 for service in self.marked_services:
                     try:

bu_isciii/bioinfo_doc.py

@@ -631,7 +631,7 @@ def send_email(self, html_text, results_pdf_file):
             server.login(user=email_host_user, password=email_host_password)
         except Exception as e:
             stderr.print("[red] Unable to send e-mail" + e)
-
+        default_cc = "[email protected]"
         msg = MIMEMultipart("alternative")
         msg["To"] = self.resolution_info["service_user_id"]["email"]
         msg["From"] = email_host_user
@@ -645,7 +645,7 @@ def send_email(self, html_text, results_pdf_file):
         )
         if bu_isciii.utils.prompt_yn_question(
             "Do you want to add any other sender? apart from %s. Note: %s is the default CC."
-            % (self.resolution_info["service_user_id"]["email"], msg["CC"].rstrip(";")),
+            % (self.resolution_info["service_user_id"]["email"], default_cc),
             dflt=False,
         ):
             stderr.print(
@@ -655,9 +655,9 @@ def send_email(self, html_text, results_pdf_file):
         else:
             cc_address = str()
         if cc_address:
-            msg["CC"] = str("[email protected];" + str(cc_address))
+            msg["CC"] = str(default_cc + ";" + str(cc_address))
         else:
-            msg["CC"] = "[email protected]"
+            msg["CC"] = default_cc
         rcpt = msg["CC"].split(";") + [msg["To"]]
         html = MIMEText(html_text, "html")
         msg.attach(html)

bu_isciii/templates/sftp_user.json

@@ -48,5 +48,6 @@
     "sresino": ["Labvirushep"],
     "svaldezate": ["Labtaxonomia"],
     "svazquez": ["Labvirusres"],
-    "ycampos": ["LabUfiecMithocondrial"]
+    "ycampos": ["LabUfiecMithocondrial"],
+    "anadonoso": ["Labenterovirus"]
 }

bu_isciii/templates/viralrecon/RESULTS/excel_generator.py

@@ -4,7 +4,7 @@
 from typing import List, Dict
 
 # conda activate viralrecon_report
-"""Standard usage: python excel_generator.py -r ./reference.tmp"""
+"""Standard usage: python excel_generator.py -r ./reference.tmp --merge_lineage_files"""
 """Single csv to excel usage: python excel_generator.py -s csv_file.csv"""
 parser = argparse.ArgumentParser(
     description="Generate excel files from viralrecon results"
@@ -22,6 +22,12 @@
     default="",
     help="Transform a single csv file to excel format. Omit rest of processes",
 )
+parser.add_argument(
+    "-l",
+    "--merge_lineage_files",
+    action="store_true",
+    help="Merge pangolin and nextclade lineage tables",
+)
 args = parser.parse_args()
 
 
@@ -135,7 +141,7 @@ def main(args):
         ref: str("ref_samples/samples_" + ref + ".tmp") for ref in references
     }
 
-    if len(references) > 1:
+    if args.merge_lineage_files:
         # Merge pangolin and nextclade csv files separatedly and create excel files for them
         merge_lineage_tables(reference_folders, samples_ref_files)
         for reference, folder in reference_folders.items():

bu_isciii/templates/viralrecon/RESULTS/viralrecon_results

@@ -26,7 +26,7 @@ ln -s ../../ANALYSIS/*/assembly_stats.csv ./assembly_stats.csv
 ln -s ../../ANALYSIS/*/01-PikaVirus-results/all_samples_virus_table_filtered.csv ./pikavirus_table.csv
 
 #conda activate viralrecon_report
-echo "python ./excel_generator.py -r ./references.tmp" > _01_generate_excel_files.sh
+echo "python ./excel_generator.py -r ./references.tmp --merge_lineage_files" > _01_generate_excel_files.sh
 #Cleaning temp files and broken symbolic links
 echo "find . -xtype l -delete" > _02_clean_folders.sh
 echo 'for dir in */; do find ${dir} -xtype l -delete; done' >> _02_clean_folders.sh
@@ -46,3 +46,12 @@ cd variants_annot; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; do a
 cd assembly_spades; rsync -rlv ../../../ANALYSIS/*/*/assembly/spades/rnaviral/*.scaffolds.fa.gz .; gunzip *.scaffolds.fa.gz; cd -
 cd abacas_assembly; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; do arr=($in); ln -s ../../../ANALYSIS/*/*${arr[1]}*/assembly/spades/rnaviral/abacas/${arr[0]}.abacas.fasta ./${arr[0]}_${arr[1]}.abacas.fasta; done; cd -
 ln -s ../../ANALYSIS/*/all_samples_filtered_BLAST_results.xlsx .
+
+"""
+Auxiliar script useful for multiple hosts if samples have pattern to distinguish:
+e.g. HOSTPATTERN = 'MONKEY'
+
+cat ../viralrecon_results | sed 's@../../@../../../@g' | sed 's/entrega01/$HOSTPATTERN_results/g' > results_wgs
+sed -i 's@ANALYSIS/\*/@ANALYSIS/*HOSTPATTERN*/@g' results_wgs.sh
+sed 's/SAMPLEPATTERN/HOSTPATTERN/g' results_wgs > results_gf.sh
+"""