Mercurial > repos > greg > pima_report
changeset 12:99613333fd1f draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 10 Mar 2023 16:35:16 +0000 |
| parents | 4a7c31f28197 |
| children | f03c80bb22e9 |
| files | pima_report.py pima_report.xml |
| diffstat | 2 files changed, 101 insertions(+), 31 deletions(-) [+] |
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--- 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()
--- 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"/>