# HG changeset patch
# User greg
# Date 1678466116 0
# Node ID 99613333fd1f98db42c1a5015d732b35a1c50862
# Parent  4a7c31f2819765fe6c1744fcdf1f70effdca75fd
Uploaded

diff -r 4a7c31f28197 -r 99613333fd1f pima_report.py
--- a/pima_report.py	Thu Mar 09 18:34:01 2023 +0000
+++ b/pima_report.py	Fri Mar 10 16:35:16 2023 +0000
@@ -16,11 +16,13 @@
 class PimaReport:
 
     def __init__(self, analysis_name=None, amr_deletions_file=None, amr_matrix_files=None, assembly_fasta_file=None,
-                 assembly_name=None, blastn_version=None, compute_sequence_length_file=None, contig_coverage_file=None,
-                 dbkey=None, dnadiff_snps_file=None, dnadiff_version=None, feature_bed_files=None, feature_png_files=None,
-                 flye_assembly_info_file=None, flye_version=None, genome_insertions_file=None, gzipped=None,
-                 illumina_fastq_file=None, kraken2_report_file=None, kraken2_version=None, mutation_regions_bed_file=None,
-                 mutation_regions_tsv_files=None, pima_css=None, plasmids_file=None, reference_insertions_file=None):
+                 assembly_name=None, bedtools_version=None, blastn_version=None, compute_sequence_length_file=None,
+                 contig_coverage_file=None, dbkey=None, dnadiff_snps_file=None, dnadiff_version=None,
+                 feature_bed_files=None, feature_png_files=None, flye_assembly_info_file=None, flye_version=None,
+                 genome_insertions_file=None, gzipped=None, illumina_fastq_file=None, kraken2_report_file=None,
+                 kraken2_version=None, minimap2_version=None, mutation_regions_bed_file=None,
+                 mutation_regions_tsv_files=None, pima_css=None, plasmids_file=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))
@@ -28,6 +30,7 @@
         self.ofh.write("analysis_name: %s\n" % str(analysis_name))
         self.ofh.write("assembly_fasta_file: %s\n" % str(assembly_fasta_file))
         self.ofh.write("assembly_name: %s\n" % str(assembly_name))
+        self.ofh.write("bedtools_version: %s\n" % str(bedtools_version))
         self.ofh.write("blastn_version: %s\n" % str(blastn_version))
         self.ofh.write("compute_sequence_length_file: %s\n" % str(compute_sequence_length_file))
         self.ofh.write("contig_coverage_file: %s\n" % str(contig_coverage_file))
@@ -43,12 +46,14 @@
         self.ofh.write("illumina_fastq_file: %s\n" % str(illumina_fastq_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("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))
         self.ofh.write("pima_css: %s\n" % str(pima_css))
         self.ofh.write("plasmids_file: %s\n" % str(plasmids_file))
-        # self.ofh.write("reference_genome: %s\n" % str(reference_genome))
         self.ofh.write("reference_insertions_file: %s\n" % str(reference_insertions_file))
+        self.ofh.write("samtools_version: %s\n" % str(samtools_version))
+        self.ofh.write("varscan_version: %s\n" % str(varscan_version))
 
         # General
         self.doc = None
@@ -57,24 +62,44 @@
         # Inputs
         self.amr_deletions_file = amr_deletions_file
         self.amr_matrix_files = amr_matrix_files
-        self.analysis_name = analysis_name
+        self.analysis_name = re.sub('_', '.', analysis_name.rstrip(' _consensus_'))
         self.assembly_fasta_file = assembly_fasta_file
-        self.assembly_name = assembly_name
-        self.blastn_version = blastn_version
+        self.assembly_name = re.sub('_', '.', assembly_name.rstrip(' _consensus_'))
+        if bedtools_version is None:
+            self.bedtools_version = 'bedtools (version unknown)'
+        else:
+            self.bedtools_version = re.sub('_', '.', bedtools_version.rstrip(' _genome insertions'))
+        if blastn_version is None:
+            self.blastn_version = 'blastn (version unknown)'
+        else:
+            self.blastn_version = re.sub('_', '.', blastn_version.rstrip(' _features_'))
         self.compute_sequence_length_file = compute_sequence_length_file
         self.contig_coverage_file = contig_coverage_file
         self.dbkey = dbkey
         self.dnadiff_snps_file = dnadiff_snps_file
-        self.dnadiff_version = dnadiff_version
+        if dnadiff_version is None:
+            self.dnadiff_version = 'dnadiff (version unknown)'
+        else:
+            self.dnadiff_version = re.sub('_', '.', dnadiff_version.rstrip(' _snps_'))
         self.feature_bed_files = feature_bed_files
         self.feature_png_files = feature_png_files
         self.flye_assembly_info_file = flye_assembly_info_file
-        self.flye_version = flye_version
+        if flye_version is None:
+            self.flye_version = 'flye (version unknown)'
+        else:
+            self.flye_version = re.sub('_', '.', flye_version.rstrip(' _assembly info_'))
         self.gzipped = gzipped
         self.genome_insertions_file = genome_insertions_file
         self.illumina_fastq_file = illumina_fastq_file
         self.kraken2_report_file = kraken2_report_file
-        self.kraken2_version = kraken2_version
+        if kraken2_version is None:
+            self.kraken2_version = 'kraken2 (version unknown)'
+        else:
+            self.kraken2_version = re.sub('_', '.', kraken2_version.rstrip(' _report_'))
+        if minimap2_version is None:
+            self.minimap2_version = 'minimap2 (version unknown)'
+        else:
+            self.minimap2_version = re.sub('_', '.', minimap2_version)
         self.mutation_regions_bed_file = mutation_regions_bed_file
         self.mutation_regions_tsv_files = mutation_regions_tsv_files
         self.read_type = 'Illumina'
@@ -83,8 +108,15 @@
         self.ont_read_count = None
         self.pima_css = pima_css
         self.plasmids_file = plasmids_file
-        # self.reference_genome = reference_genome
         self.reference_insertions_file = reference_insertions_file
+        if samtools_version is None:
+            self.samtools_version = 'samtools (version unknown)'
+        else:
+            self.samtools_version = re.sub('_', '.', samtools_version)
+        if varscan_version is None:
+            self.varscan_version = 'varscan (version unknown)'
+        else:
+            self.varscan_version = re.sub('_', '.', varscan_version)
 
         # Titles
         self.alignment_title = 'Comparison with reference'
@@ -522,9 +554,8 @@
                 self.doc.new_line()
                 self.ofh.write("Before new_table, len(Table_List):: %s\n" % str(len(Table_List)))
                 self.doc.new_table(columns=5, rows=row_count, text=Table_List, text_align='left')
-        if self.blastn_version is not None:
-            blastn_version = 'The genome assembly was queried for features using %s.' % self.blastn_version
-        bedtools_version = 'Feature hits were clustered using bedtools and the highest scoring hit for each cluster was reported.'
+        blastn_version = 'The genome assembly was queried for features using %s.' % self.blastn_version
+        bedtools_version = 'Feature hits were clustered using %s and the highest scoring hit for each cluster was reported.' % self.bedtools_version
         method = '%s  %s' % (blastn_version, bedtools_version)
         self.methods[self.feature_methods_title] = self.methods[self.feature_methods_title].append(pandas.Series(method))
 
@@ -610,9 +641,9 @@
                     Table_List = Table_List + region_mutations.iloc[i, [0, 1, 3, 4, 5, 6]].values.tolist()
                 row_count = int(len(Table_List) / 6)
                 self.doc.new_table(columns=6, rows=row_count, text=Table_List, text_align='left')
-        method = '%s reads were mapped to the reference sequence using minimap2.' % self.read_type
+        method = '%s reads were mapped to the reference sequence using %s.' % (self.read_type, self.minimap2_version)
         self.methods[self.mutation_methods_title] = self.methods[self.mutation_methods_title].append(pandas.Series(method))
-        method = 'Mutations were identified using samtools mpileup and varscan.'
+        method = 'Mutations were identified using %s mpileup and %s.' % (self.samtools_version, self.varscan_version)
         self.methods[self.mutation_methods_title] = self.methods[self.mutation_methods_title].append(pandas.Series(method))
 
     def add_amr_matrix(self):
@@ -676,7 +707,7 @@
                 Table_List = Table_List + genome_indels.iloc[i, :].values.tolist()
             row_count = int(len(Table_List) / 4)
             self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left')
-        method = 'Large insertions or deletions were found as the complement of aligned regions using bedtools.'
+        method = 'Large insertions or deletions were found as the complement of aligned regions using %s.' % self.bedtools_version
         self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(pandas.Series(method))
         self.doc.new_line()
         self.doc.new_line('<div style="page-break-after: always;"></div>')
@@ -701,7 +732,7 @@
             Table_List = Table_List + plasmids.iloc[i, 0:6].values.tolist()
         row_count = int(len(Table_List) / 6)
         self.doc.new_table(columns=6, rows=row_count, text=Table_List, text_align='left')
-        method = 'The plasmid reference database was queried against the genome assembly using minimap2.'
+        method = 'The plasmid reference database was queried against the genome assembly using %s.' % self.minimap2_version
         self.methods[self.plasmid_methods_title] = self.methods[self.plasmid_methods_title].append(pandas.Series(method))
         method = 'The resulting BAM was converted to a PSL using a custom version of sam2psl.'
         self.methods[self.plasmid_methods_title] = self.methods[self.plasmid_methods_title].append(pandas.Series(method))
@@ -802,12 +833,13 @@
 parser.add_argument('--analysis_name', action='store', dest='analysis_name', help='Sample identifier')
 parser.add_argument('--assembly_fasta_file', action='store', dest='assembly_fasta_file', help='Assembly fasta file')
 parser.add_argument('--assembly_name', action='store', dest='assembly_name', help='Assembly identifier')
+parser.add_argument('--bedtools_version', action='store', dest='bedtools_version', default=None, help='Bedtools version string')
 parser.add_argument('--blastn_version', action='store', dest='blastn_version', default=None, help='Blastn version string')
 parser.add_argument('--compute_sequence_length_file', action='store', dest='compute_sequence_length_file', help='Comnpute sequence length tabular file')
 parser.add_argument('--contig_coverage_file', action='store', dest='contig_coverage_file', help='Contig coverage TSV file')
 parser.add_argument('--dbkey', action='store', dest='dbkey', help='Reference genome identifier')
 parser.add_argument('--dnadiff_snps_file', action='store', dest='dnadiff_snps_file', help='DNAdiff snps tabular file')
-parser.add_argument('--dnadiff_version', action='store', dest='dnadiff_version', help='DNAdiff version string')
+parser.add_argument('--dnadiff_version', action='store', dest='dnadiff_version', default=None, help='DNAdiff version string')
 parser.add_argument('--feature_bed_dir', action='store', dest='feature_bed_dir', help='Directory of best feature hits bed files')
 parser.add_argument('--feature_png_dir', action='store', dest='feature_png_dir', help='Directory of best feature hits png files')
 parser.add_argument('--flye_assembly_info_file', action='store', dest='flye_assembly_info_file', default=None, help='Flye assembly info tabular file')
@@ -817,12 +849,14 @@
 parser.add_argument('--illumina_fastq_file', action='store', dest='illumina_fastq_file', help='Input sample')
 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('--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')
 parser.add_argument('--pima_css', action='store', dest='pima_css', help='PIMA css stypesheet')
 parser.add_argument('--plasmids_file', action='store', dest='plasmids_file', help='pChunks plasmids TSV file')
 parser.add_argument('--reference_insertions_file', action='store', dest='reference_insertions_file', help='Reference insertions BED file')
-# parser.add_argument('--reference_genome', action='store', dest='reference_genome', help='Reference genome fasta file')
+parser.add_argument('--samtools_version', action='store', dest='samtools_version', default=None, help='Samtools version string')
+parser.add_argument('--varscan_version', action='store', dest='varscan_version', default=None, help='Varscan version string')
 
 args = parser.parse_args()
 
@@ -852,6 +886,7 @@
                              amr_matrix_files,
                              args.assembly_fasta_file,
                              args.assembly_name,
+                             args.bedtools_version,
                              args.blastn_version,
                              args.compute_sequence_length_file,
                              args.contig_coverage_file,
@@ -867,9 +902,12 @@
                              args.illumina_fastq_file,
                              args.kraken2_report_file,
                              args.kraken2_version,
+                             args.minimap2_version,
                              args.mutation_regions_bed_file,
                              mutation_regions_files,
                              args.pima_css,
                              args.plasmids_file,
-                             args.reference_insertions_file)
+                             args.reference_insertions_file,
+                             args.samtools_version,
+                             args.varscan_version)
 markdown_report.make_report()
diff -r 4a7c31f28197 -r 99613333fd1f pima_report.xml
--- a/pima_report.xml	Thu Mar 09 18:34:01 2023 +0000
+++ b/pima_report.xml	Fri Mar 10 16:35:16 2023 +0000
@@ -10,17 +10,29 @@
 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
 
-#set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
-#set blastn_version = $blastn_version.rstrip('(features)')
-#set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
-#set dnadiff_version = $dnadiff_version.rstrip('(snps)')
+#if str($bedtools_complementbed_file) not in ['None', '']:
+    #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
+#end if
+#if str($blastn_features) not in ['None', '']:
+    #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
+#end if
+#if str($dnadiff_snps_file) not in ['None', '']:
+    #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
+#end if
 #if str($flye_assembly_info_file) not in ['None', '']:
     #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
-    #set flye_version = $flye_version.rstrip('(assembly info)')
 #end if
 #if str($kraken2_report_file) not in ['None', '']:
     #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
-    #set kraken2_version = $kraken2_version.rstrip('(report)')
+#end if
+#if str($minimap2_bam_file) not in ['None', '']:
+    #set minimap2_version = re.sub('[^\s\w\-]', '_', str($minimap2_bam_file.element_identifier))
+#end if
+#if str($samtools_pileup_file) not in ['None', '']:
+    #set samtools_version = re.sub('[^\s\w\-]', '_', str($samtools_pileup_file.element_identifier))
+#end if
+#if str($varscan_vcf_file) not in ['None', '']:
+    #set varscan_version = re.sub('[^\s\w\-]', '_', str($varscan_vcf_file.element_identifier))
 #end if
 
 mkdir amr_matrix_png_dir &&
@@ -56,12 +68,19 @@
 --analysis_name '$analysis_name'
 --assembly_fasta_file '$assembly_fasta_file'
 --assembly_name '$assembly_name'
---blastn_version '$blastn_version'
+#if str($bedtools_complementbed_file) not in ['None', '']:
+    --bedtools_version '$bedtools_version'
+#end if
+#if str($blastn_features) not in ['None', '']:
+    --blastn_version '$blastn_version'
+#end if
 --compute_sequence_length_file '$compute_sequence_length_file'
 --contig_coverage_file '$contig_coverage_file'
 --dbkey '$aligned_sample.metadata.dbkey'
 --dnadiff_snps_file '$dnadiff_snps_file'
---dnadiff_version '$dnadiff_version'
+#if str($dnadiff_snps_file) not in ['None', '']:
+    --dnadiff_version '$dnadiff_version'
+#end if
 --feature_bed_dir 'feature_bed_dir'
 --feature_png_dir 'feature_png_dir'
 #if str($flye_assembly_info_file) not in ['None', '']:
@@ -77,11 +96,20 @@
     --kraken2_report_file '$kraken2_report_file'
     --kraken2_version '$kraken2_version'
 #end if
+#if str($minimap2_bam_file) not in ['None', '']:
+    --minimap2_version '$minimap2_version'
+#end if
 --mutation_regions_dir 'mutation_regions_dir'
 --mutation_regions_bed_file '$mutation_regions_bed_file'
 --pima_css '${__tool_directory__}/pima.css'
 --plasmids_file '$plasmids_file'
 --reference_insertions_file '$reference_insertions_file'
+#if str($samtools_pileup_file) not in ['None', '']:
+    --samtools_version '$samtools_version'
+#end if
+#if str($varscan_vcf_file) not in ['None', '']:
+    --varscan_version '$varscan_version'
+#end if
 && mv 'pima_report.pdf' '$output'
     ]]></command>
     <inputs>
@@ -89,6 +117,7 @@
         <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
         <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
         <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
+        <param name="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/>
         <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/>
         <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
         <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
@@ -99,10 +128,13 @@
         <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="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
+        <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"/>
         <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
         <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
+        <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>
+        <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/>
     </inputs>
     <outputs>
         <data name="output" format="pdf"/>