Mercurial > repos > greg > pima_report
changeset 31:a859de7cce94 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 27 Jun 2023 13:39:14 +0000 |
| parents | 134a0879d0b6 |
| children | 163260afc1b1 |
| files | pima_report.py |
| diffstat | 1 files changed, 4 insertions(+), 89 deletions(-) [+] |
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--- a/pima_report.py Wed May 03 15:36:36 2023 +0000 +++ b/pima_report.py Tue Jun 27 13:39:14 2023 +0000 @@ -29,46 +29,6 @@ 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)) - self.ofh.write("amr_matrix_files: %s\n" % str(amr_matrix_files)) - self.ofh.write("analysis_name: %s\n" % str(analysis_name)) - self.ofh.write("assembler_version: %s\n" % str(assembler_version)) - 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("circos_files: %s\n" % str(circos_files)) - 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)) - self.ofh.write("dbkey: %s\n" % str(dbkey)) - self.ofh.write("dnadiff_snps_file: %s\n" % str(dnadiff_snps_file)) - self.ofh.write("dnadiff_version: %s\n" % str(dnadiff_version)) - self.ofh.write("errors_file: %s\n" % str(errors_file)) - self.ofh.write("feature_bed_files: %s\n" % str(feature_bed_files)) - self.ofh.write("feature_png_files: %s\n" % str(feature_png_files)) - self.ofh.write("flye_assembly_info_file: %s\n" % str(flye_assembly_info_file)) - self.ofh.write("gzipped: %s\n" % str(gzipped)) - self.ofh.write("genome_insertions_file: %s\n" % str(genome_insertions_file)) - self.ofh.write("illumina_forward_read_file: %s\n" % str(illumina_forward_read_file)) - 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)) - self.ofh.write("ont_file: %s\n" % str(ont_file)) - self.ofh.write("pima_css: %s\n" % str(pima_css)) - self.ofh.write("plasmids_file: %s\n" % str(plasmids_file)) - self.ofh.write("quast_report_file: %s\n" % str(quast_report_file)) - self.ofh.write("read_type: %s\n" % str(read_type)) - 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 @@ -78,7 +38,6 @@ self.amr_deletions_file = amr_deletions_file self.amr_matrix_files = amr_matrix_files self.analysis_name = analysis_name.split('_')[0] - self.ofh.write("self.analysis_name: %s\n" % str(self.analysis_name)) if assembler_version is None: self.assembler_version = 'assembler (version unknown)' else: @@ -217,7 +176,6 @@ # Actions self.did_guppy_ont_fast5 = False self.did_qcat_ont_fastq = False - self.ofh.write("self.read_type: %s\n" % str(self.read_type)) if self.read_type == 'ONT': self.info_ont_fastq(self.ont_file) else: @@ -225,7 +183,6 @@ self.load_contig_info() def run_command(self, command): - self.ofh.write("\nXXXXXX In run_command, command:\n%s\n\n" % str(command)) try: return re.split('\\n', subprocess.check_output(command, shell=True).decode('utf-8')) except Exception: @@ -233,8 +190,6 @@ sys.exit(message) def format_kmg(self, number, decimals=0): - self.ofh.write("\nXXXXXX In format_kmg, number:\n%s\n" % str(number)) - self.ofh.write("XXXXXX In format_kmg, decimals:\n%s\n\n" % str(decimals)) if number == 0: return '0' magnitude_powers = [10**9, 10**6, 10**3, 1] @@ -279,7 +234,6 @@ self.assembly_size = self.format_kmg(sum([len(x) for x in self.assembly]), decimals=1) def info_illumina_fastq(self, illumina_read_files): - self.ofh.write("\nXXXXXX In info_illumina_fastq\n\n") if self.gzipped: opener = 'gunzip -c' else: @@ -288,21 +242,14 @@ command = ' '.join([opener, fastq_file, '| awk \'{getline;s += length($1);getline;getline;}END{print s/(NR/4)"\t"(NR/4)"\t"s}\'']) - output = self.run_command(command) - self.ofh.write("output:\n%s\n" % str(output)) - self.ofh.write("re.split('\\t', self.run_command(command)[0]:\n%s\n" % str(re.split('\\t', self.run_command(command)[0]))) values = [] for i in re.split('\\t', self.run_command(command)[0]): if i == '': values.append(float('nan')) else: values.append(float(i)) - self.ofh.write("values:\n%s\n" % str(values)) - self.ofh.write("values[0]:\n%s\n" % str(values[0])) self.illumina_length_mean += values[0] - self.ofh.write("values[1]:\n%s\n" % str(values[1])) self.illumina_read_count += int(values[1]) - self.ofh.write("values[2]:\n%s\n" % str(values[2])) self.illumina_bases += int(values[2]) self.illumina_length_mean /= 2 self.illumina_bases = self.format_kmg(self.illumina_bases, decimals=1) @@ -318,7 +265,6 @@ self.doc.new_line() def add_run_information(self): - self.ofh.write("\nXXXXXX In add_run_information\n\n") self.doc.new_line() self.doc.new_header(1, 'Run information') # Tables in md.utils are implemented as a wrapping function. @@ -345,7 +291,6 @@ self.doc.new_line() def add_ont_library_information(self): - self.ofh.write("\nXXXXXX In add_ont_library_information\n\n") if self.ont_n50 is None: return self.doc.new_line() @@ -370,7 +315,6 @@ self.doc.new_line() def add_illumina_library_information(self): - self.ofh.write("\nXXXXXX In add_illumina_library_information\n\n") if self.illumina_length_mean is None: return self.doc.new_line() @@ -402,7 +346,6 @@ self.assembly_notes = self.assembly_notes.append(pandas.Series(warning)) def add_assembly_information(self): - self.ofh.write("\nXXXXXX In add_assembly_information\n\n") if self.assembly_fasta_file is None: return self.load_assembly() @@ -419,7 +362,6 @@ self.doc.new_table(columns=2, rows=3, text=Table_List, text_align='left') def info_ont_fastq(self, fastq_file): - self.ofh.write("\nXXXXXX In info_ont_fastq, fastq_file:\n%s\n\n" % str(fastq_file)) opener = 'cat' if self.gzipped: opener = 'gunzip -c' @@ -469,7 +411,6 @@ return string def add_contig_info(self): - self.ofh.write("\nXXXXXX In add_contig_info\n\n") if self.contig_info is None or self.read_type not in self.contig_info.index: return self.doc.new_line() @@ -483,7 +424,6 @@ self.doc.new_table(columns=3, rows=row_count, text=Table_List, text_align='left') def add_assembly_notes(self): - self.ofh.write("\nXXXXXX In add_assembly_notes\n\n") if len(self.assembly_notes) == 0: return self.doc.new_line() @@ -494,7 +434,6 @@ self.doc.new_line(note) def add_contamination(self): - self.ofh.write("\nXXXXXX In add_contamination\n\n") if self.kraken2_report_file is None: return # Read in the Kraken fractions and pull out the useful parts @@ -522,7 +461,6 @@ self.methods[self.contamination_methods_title] = self.methods[self.contamination_methods_title].append(pandas.Series(method)) def add_alignment(self): - self.ofh.write("\nXXXXXX In add_alignment\n\n") if self.quast_report_file is not None: # Process quast values. quast_report = pandas.read_csv(self.quast_report_file, header=0, index_col=0, sep='\t') @@ -555,7 +493,7 @@ contig_title = 'Alignment to %s' % contig self.doc.new_line() self.doc.new_header(level=3, title=contig_title) - self.doc.new_line('Blue color indicates query sequences aligned to the reference sequence, which is shown in yellow') + self.doc.new_line('Blue indicates query sequences aligned to the reference sequence, yellow indicates no alignment') self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(circos_file))) self.doc.new_line('<div style="page-break-after: always;"></div>') self.doc.new_line() @@ -569,7 +507,6 @@ self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(pandas.Series(method)) def add_features(self): - self.ofh.write("\nXXXXXX In add_features\n\n") if len(self.feature_bed_files) == 0: return for bbf in self.feature_bed_files: @@ -578,13 +515,10 @@ self.feature_hits[os.path.basename(bbf)] = best if len(self.feature_hits) == 0: return - self.ofh.write("self.feature_hits: %s\n" % str(self.feature_hits)) self.doc.new_line() self.doc.new_header(level=2, title=self.feature_title) for feature_name in self.feature_hits.index.tolist(): - self.ofh.write("feature_name: %s\n" % str(feature_name)) features = self.feature_hits[feature_name].copy() - self.ofh.write("features: %s\n" % str(features)) if features.shape[0] == 0: continue features.iloc[:, 1] = features.iloc[:, 1].apply(lambda x: '{:,}'.format(x)) @@ -594,23 +528,15 @@ if (features.shape[0] == 0): continue for contig in pandas.unique(features.iloc[:, 0]): - self.ofh.write("contig: %s\n" % str(contig)) self.doc.new_line(contig) contig_features = features.loc[(features.iloc[:, 0] == contig), :] - self.ofh.write("contig_features: %s\n" % str(contig_features)) Table_List = ['Start', 'Stop', 'Feature', 'Identity (%)', 'Strand'] for i in range(contig_features.shape[0]): - self.ofh.write("i: %s\n" % str(i)) feature = contig_features.iloc[i, :].copy(deep=True) - self.ofh.write("feature: %s\n" % str(feature)) feature[4] = '{:.3f}'.format(feature[4]) - self.ofh.write("feature[1:].values.tolist(): %s\n" % str(feature[1:].values.tolist())) Table_List = Table_List + feature[1:].values.tolist() - self.ofh.write("Table_List: %s\n" % str(Table_List)) row_count = int(len(Table_List) / 5) - self.ofh.write("row_count: %s\n" % str(row_count)) 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') 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 @@ -618,7 +544,6 @@ self.methods[self.feature_methods_title] = self.methods[self.feature_methods_title].append(pandas.Series(method)) def add_feature_plots(self): - self.ofh.write("\nXXXXXX In add_feature_plots\n\n") if len(self.feature_png_files) == 0: return self.doc.new_line() @@ -628,7 +553,6 @@ self.doc.new_line(self.doc.new_inline_image(text='Analysis', path=os.path.abspath(feature_png_file))) def add_mutations(self): - self.ofh.write("\nXXXXXX In add_mutations\n\n") if len(self.mutation_regions_tsv_files) == 0: return try: @@ -640,7 +564,6 @@ for region_i in range(mutation_regions.shape[0]): region = mutation_regions.iloc[region_i, :] region_name = str(region['name']) - self.ofh.write("Processing mutations for region %s\n" % region_name) region_mutations_tsv_name = '%s_mutations.tsv' % region_name if region_mutations_tsv_name not in self.mutation_regions_tsv_files: continue @@ -692,19 +615,17 @@ self.methods[self.mutation_methods_title] = self.methods[self.mutation_methods_title].append(pandas.Series(method)) def add_amr_matrix(self): - self.ofh.write("\nXXXXXX In add_amr_matrix\n\n") # Make sure that we have an AMR matrix to plot if len(self.amr_matrix_files) == 0: return self.doc.new_line() self.doc.new_header(level=2, title=self.amr_matrix_title) - self.doc.new_line('AMR genes and mutations with their corresponding drugs') + amr_matrix_text = 'AMR genes and mutations with their corresponding drugs: dark blue indicates the presence of a gene/mutation, light blue indicates the absence of a gene/mutation' + self.doc.new_line(amr_matrix_text) for amr_matrix_file in self.amr_matrix_files: - self.doc.new_line(self.doc.new_inline_image(text='AMR genes and mutations with their corresponding drugs', - path=os.path.abspath(amr_matrix_file))) + self.doc.new_line(self.doc.new_inline_image(text=amr_matrix_text, path=os.path.abspath(amr_matrix_file))) def add_large_indels(self): - self.ofh.write("\nXXXXXX In add_large_indels\n\n") large_indels = pandas.Series(dtype='float64') # Pull in insertions. try: @@ -751,7 +672,6 @@ 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 if not os.path.isfile(self.lrn_risk_amr_file) and not os.path.isfile(self.lrn_risk_blacklist_file) and not os.path.isfile(self.lrn_risk_vf_file): @@ -832,7 +752,6 @@ self.methods[self.plasmid_methods_title] = self.methods[self.plasmid_methods_title].append(pandas.Series(method)) def add_methods(self): - self.ofh.write("\nXXXXXX In add_methods\n\n") if len(self.methods) == 0: return self.doc.new_line() @@ -847,7 +766,6 @@ self.doc.new_line() def add_summary(self): - self.ofh.write("\nXXXXXX In add_summary\n\n") # Add summary title self.doc.new_header(level=1, title=self.summary_title) # First section of Summary @@ -893,7 +811,6 @@ self.doc.create_md_file() def make_report(self): - self.ofh.write("\nXXXXXX In make_report\n\n") self.start_doc() self.add_summary() self.add_contamination() @@ -912,12 +829,10 @@ # (implied) argument in the following command must be 'html' instead of # the more logical 'pdf'. see the answer from snsn in this thread: # https://github.com/jessicategner/pypandoc/issues/186 - self.ofh.write("\nXXXXX In make_report, calling pypandoc.convert_file...\n\n") pypandoc.convert_file(self.report_md, 'html', extra_args=['--pdf-engine=weasyprint', '-V', '-css=%s' % self.pima_css], outputfile='pima_report.pdf') - self.ofh.close() parser = argparse.ArgumentParser()