# HG changeset patch
# User greg
# Date 1682710858 0
# Node ID 27485e70ed2b0e120d74780fe9be472e0c1ba1bf
# Parent  ddc056cf16bf0b04c2c03c76215b9119b2f22cb2
Uploaded

diff -r ddc056cf16bf -r 27485e70ed2b pima_report.py
--- a/pima_report.py	Tue Apr 25 21:30:56 2023 +0000
+++ b/pima_report.py	Fri Apr 28 19:40:58 2023 +0000
@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 import argparse
 import os
 import pandas
@@ -23,9 +25,10 @@
                  dnadiff_snps_file=None, dnadiff_version=None, errors_file=None, feature_bed_files=None,
                  feature_png_files=None, flye_assembly_info_file=None, genome_insertions_file=None, gzipped=None,
                  illumina_forward_read_file=None, illumina_reverse_read_file=None, kraken2_report_file=None,
-                 kraken2_version=None, minimap2_version=None, mutation_regions_bed_file=None,
-                 mutation_regions_tsv_files=None, ont_file=None, pima_css=None, plasmids_file=None, quast_report_file=None,
-                 read_type=None, reference_insertions_file=None, samtools_version=None, varscan_version=None):
+                 kraken2_version=None, lrn_risk_amr_file=None, lrn_risk_blacklist_file=None, lrn_risk_vf_file=None,
+                 minimap2_version=None, mutation_regions_bed_file=None, mutation_regions_tsv_files=None,
+                 ont_file=None, pima_css=None, plasmids_file=None, quast_report_file=None, read_type=None,
+                 reference_insertions_file=None, samtools_version=None, varscan_version=None):
         self.ofh = open("process_log.txt", "w")
 
         self.ofh.write("amr_deletions_file: %s\n" % str(amr_deletions_file))
@@ -52,6 +55,9 @@
         self.ofh.write("illumina_reverse_read_file: %s\n" % str(illumina_reverse_read_file))
         self.ofh.write("kraken2_report_file: %s\n" % str(kraken2_report_file))
         self.ofh.write("kraken2_version: %s\n" % str(kraken2_version))
+        self.ofh.write("lrn_risk_amr_file: %s\n" % str(lrn_risk_amr_file))
+        self.ofh.write("lrn_risk_blacklist_file: %s\n" % str(lrn_risk_blacklist_file))
+        self.ofh.write("lrn_risk_vf_file: %s\n" % str(lrn_risk_vf_file))
         self.ofh.write("minimap2_version: %s\n" % str(minimap2_version))
         self.ofh.write("mutation_regions_bed_file: %s\n" % str(mutation_regions_bed_file))
         self.ofh.write("mutation_regions_tsv_files: %s\n" % str(mutation_regions_tsv_files))
@@ -115,6 +121,9 @@
             self.kraken2_version = 'kraken2 (version unknown)'
         else:
             self.kraken2_version = re.sub('_', '.', kraken2_version.rstrip(' _report_'))
+        self.lrn_risk_amr_file = lrn_risk_amr_file
+        self.lrn_risk_blacklist_file = lrn_risk_blacklist_file
+        self.lrn_risk_vf_file = lrn_risk_vf_file
         if minimap2_version is None:
             self.minimap2_version = 'minimap2 (version unknown)'
         else:
@@ -150,6 +159,7 @@
         self.feature_methods_title = 'Feature annotation'
         self.feature_plot_title = 'Feature annotation plots'
         self.large_indel_title = 'Large insertions & deletions'
+        self.lrn_risk_title = 'LRNRisk isolate classification'
         self.methods_title = 'Methods'
         self.mutation_errors_title = 'Errors finding mutations in the sample'
         self.mutation_title = 'Mutations found in the sample'
@@ -740,6 +750,57 @@
         self.doc.new_line('<div style="page-break-after: always;"></div>')
         self.doc.new_line()
 
+    def add_lrn_risk_info(self):
+        self.ofh.write("\nXXXXXX In add_lrn_risk_info\n\n")
+        if self.lrn_risk_amr_file is None and self.lrn_risk_blacklist_file is None and self.lrn_risk_vf_file is None:
+            return
+        self.doc.new_line()
+        self.doc.new_header(level=2, title=self.lrn_risk_title)
+        # Process self.lrn_risk_amr_file.
+        try:
+            lrn_risk_amr = pandas.read_csv(filepath_or_buffer=self.lrn_risk_amr_file, sep='\t', header=0)
+        except Exception:
+            lrn_risk_amr = pandas.DataFrame()
+        if lrn_risk_amr.shape[0] > 0:
+            self.doc.new_line()
+            self.doc.new_header(level=2, title="AMR Determinant Distribution")
+            self.doc.new_line()
+            Table_List = ["Gene", "Contig", "% Identity", "% Coverage", "E-Value", "Annotation", "Comparison to Publicly Available Genomes"]
+            for index, row in lrn_risk_amr.iterrows():
+                Table_List = Table_List + row.tolist()
+            row_count = int(len(Table_List) / 7)
+            self.doc.new_table(columns=7, rows=row_count, text=Table_List, text_align='left')
+        # Process self.lrn_risk_blacklist_file.
+        try:
+            lrn_risk_blacklist = pandas.read_csv(filepath_or_buffer=self.lrn_risk_blacklist_file, sep='\t', header=0)
+        except Exception:
+            lrn_risk_blacklist = pandas.DataFrame()
+        if lrn_risk_blacklist.shape[0] > 0:
+            self.doc.new_line()
+            self.doc.new_header(level=2, title="Blacklisted High-risk Virulence Factors")
+            self.doc.new_line()
+            Table_List = ["Blacklisted Gene", "Reason", "Risk Category"]
+            for index, row in lrn_risk_blacklist.iterrows():
+                Table_List = Table_List + row.tolist()
+            row_count = int(len(Table_List) / 3)
+            self.doc.new_table(columns=3, rows=row_count, text=Table_List, text_align='left')
+        # Process self.lrn_risk_vf_file.
+        try:
+            lrn_risk_vf = pandas.read_csv(filepath_or_buffer=self.lrn_risk_vf_file, sep='\t', header=0)
+        except Exception:
+            lrn_risk_vf = pandas.DataFrame()
+        if lrn_risk_vf.shape[0] > 0:
+            self.doc.new_line()
+            self.doc.new_header(level=2, title="Virulence Factor Distribution")
+            self.doc.new_line()
+            Table_List = ["Gene", "Contig", "% Identity", "% Coverage", "E-Value", "Annotation", "Comparison to Publicly Available Genomes"]
+            for index, row in lrn_risk_vf.iterrows():
+                Table_List = Table_List + row.tolist()
+            row_count = int(len(Table_List) / 7)
+            self.doc.new_table(columns=7, rows=row_count, text=Table_List, text_align='left')
+        self.doc.new_line('<div style="page-break-after: always;"></div>')
+        self.doc.new_line()
+
     def add_plasmids(self):
         try:
             plasmids = pandas.read_csv(filepath_or_buffer=self.plasmids_file, sep='\t', header=0)
@@ -839,6 +900,7 @@
         self.add_large_indels()
         self.add_plasmids()
         self.add_amr_matrix()
+        self.add_lrn_risk_info()
         # self.add_snps()
         self.add_methods()
         self.make_tex()
@@ -880,6 +942,9 @@
 parser.add_argument('--illumina_reverse_read_file', action='store', dest='illumina_reverse_read_file', help='Illumina reverse read file')
 parser.add_argument('--kraken2_report_file', action='store', dest='kraken2_report_file', default=None, help='kraken2 report file')
 parser.add_argument('--kraken2_version', action='store', dest='kraken2_version', default=None, help='kraken2 version string')
+parser.add_argument('--lrn_risk_amr_file', action='store', dest='lrn_risk_amr_file', default=None, help='LRN RISK AMR TSV file')
+parser.add_argument('--lrn_risk_blacklist_file', action='store', dest='lrn_risk_blacklist_file', default=None, help='LRN RISK blacklist TSV file')
+parser.add_argument('--lrn_risk_vf_file', action='store', dest='lrn_risk_vf_file', default=None, help='LRN RISK virulence factors TSV file')
 parser.add_argument('--minimap2_version', action='store', dest='minimap2_version', default=None, help='minimap2 version string')
 parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file')
 parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files')
@@ -944,6 +1009,9 @@
                              args.illumina_reverse_read_file,
                              args.kraken2_report_file,
                              args.kraken2_version,
+                             args.lrn_risk_amr_file,
+                             args.lrn_risk_blacklist_file,
+                             args.lrn_risk_vf_file,
                              args.minimap2_version,
                              args.mutation_regions_bed_file,
                              mutation_regions_files,
diff -r ddc056cf16bf -r 27485e70ed2b pima_report.xml
--- a/pima_report.xml	Tue Apr 25 21:30:56 2023 +0000
+++ b/pima_report.xml	Fri Apr 28 19:40:58 2023 +0000
@@ -83,6 +83,30 @@
     ln -s $i 'mutation_regions_dir/$identifier' &&
 #end for
 
+#if $lrn_risk_amr_collection:
+    #set lrn_risk_amr_file = 'lrn_risk_amr.tsv'
+    touch $lrn_risk_amr_file &&
+    #for $i in $lrn_risk_amr_collection:
+        cat $i >> $lrn_risk_amr_file &&
+    #end for
+#end if
+
+#if $lrn_risk_blacklist_collection:
+    #set lrn_risk_blacklist_file = 'lrn_risk_blacklist.tsv'
+    touch $lrn_risk_blacklist_file &&
+    #for $i in $lrn_risk_blacklist_collection:
+        cat $i >> $lrn_risk_blacklist_file &&
+    #end for
+#end if
+
+#if $lrn_risk_vf_collection:
+    #set lrn_risk_vf_file = 'lrn_risk_vf.tsv'
+    touch $lrn_risk_vf_file &&
+    #for $i in $lrn_risk_vf_collection:
+        cat $i >> $lrn_risk_vf_file &&
+    #end for
+#end if
+
 python '${__tool_directory__}/pima_report.py' 
 --amr_matrix_png_dir 'amr_matrix_png_dir'
 --amr_deletions_file '$amr_deletions_file'
@@ -132,6 +156,15 @@
     --kraken2_report_file '$kraken2_report_file'
     --kraken2_version '$kraken2_version'
 #end if
+#if $lrn_risk_amr_collection:
+    --lrn_risk_amr_file '$lrn_risk_amr_file'
+#end if
+#if $lrn_risk_blacklist_collection:
+    --lrn_risk_blacklist_file '$lrn_risk_blacklist_file'
+#end if
+#if $lrn_risk_vf_collection:
+    --lrn_risk_vf_file '$lrn_risk_vf_file'
+#end if
 #if str($minimap2_bam_file) not in ['None', '']:
     --minimap2_version '$minimap2_version'
 #end if
@@ -167,6 +200,9 @@
         <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
         <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
         <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
+        <param name="lrn_risk_amr_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk AMR collection"/>
+        <param name="lrn_risk_blacklist_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk blacklist collection"/>
+        <param name="lrn_risk_vf_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk virulence factors collection"/>
         <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
         <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
         <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>