# HG changeset patch
# User greg
# Date 1678977733 0
# Node ID f03c80bb22e9c032f0fa2c7daa6c6ea739c772ca
# Parent 99613333fd1f98db42c1a5015d732b35a1c50862
Uploaded
diff -r 99613333fd1f -r f03c80bb22e9 pima_report.py
--- a/pima_report.py Fri Mar 10 16:35:16 2023 +0000
+++ b/pima_report.py Thu Mar 16 14:42:13 2023 +0000
@@ -16,13 +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, 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):
+ assembly_name=None, bedtools_version=None, blastn_version=None, circos_files=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, quast_report_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))
@@ -32,6 +32,7 @@
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))
@@ -51,6 +52,7 @@
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("quast_report_file: %s\n" % str(quast_report_file))
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))
@@ -62,7 +64,8 @@
# Inputs
self.amr_deletions_file = amr_deletions_file
self.amr_matrix_files = amr_matrix_files
- self.analysis_name = re.sub('_', '.', analysis_name.rstrip(' _consensus_'))
+ self.analysis_name = analysis_name.split('_')[0]
+ self.ofh.write("self.analysis_name: %s\n" % str(self.analysis_name))
self.assembly_fasta_file = assembly_fasta_file
self.assembly_name = re.sub('_', '.', assembly_name.rstrip(' _consensus_'))
if bedtools_version is None:
@@ -73,6 +76,7 @@
self.blastn_version = 'blastn (version unknown)'
else:
self.blastn_version = re.sub('_', '.', blastn_version.rstrip(' _features_'))
+ self.circos_files = circos_files
self.compute_sequence_length_file = compute_sequence_length_file
self.contig_coverage_file = contig_coverage_file
self.dbkey = dbkey
@@ -108,6 +112,8 @@
self.ont_read_count = None
self.pima_css = pima_css
self.plasmids_file = plasmids_file
+ self.quast_report_file = quast_report_file
+ self.reference_insertions_file = reference_insertions_file
self.reference_insertions_file = reference_insertions_file
if samtools_version is None:
self.samtools_version = 'samtools (version unknown)'
@@ -139,7 +145,7 @@
self.plasmid_title = 'Plasmid annotation'
self.reference_methods_title = 'Reference comparison'
self.snp_indel_title = 'SNPs and small indels'
- self.summary_title = 'Analysis of %s' % analysis_name
+ self.summary_title = 'Summary'
# Methods
self.methods = pandas.Series(dtype='float64')
@@ -163,13 +169,9 @@
self.illumina_length_mean = 0
self.illumina_read_count = 0
self.illumina_bases = 0
- self.mean_coverage = 0
- self.num_assembly_contigs = 0
# TODO: should the following 2 values be passed as parameters?
self.ont_n50_min = 2500
self.ont_coverage_min = 30
- self.quast_indels = 0
- self.quast_mismatches = 0
# Actions
self.did_guppy_ont_fast5 = False
@@ -265,7 +267,8 @@
self.illumina_bases = self.format_kmg(self.illumina_bases, decimals=1)
def start_doc(self):
- self.doc = MdUtils(file_name=self.report_md, title='')
+ header_text = 'Analysis of ' + self.analysis_name
+ self.doc = MdUtils(file_name=self.report_md, title=header_text)
def add_run_information(self):
self.ofh.write("\nXXXXXX In add_run_information\n\n")
@@ -319,7 +322,7 @@
def add_illumina_library_information(self):
self.ofh.write("\nXXXXXX In add_illumina_library_information\n\n")
- if self.illumina_length_mean is None:
+ if self.illumina_length_mean == 0:
return
self.doc.new_line()
self.doc.new_header(2, 'Illumina library statistics')
@@ -475,38 +478,41 @@
def add_alignment(self):
self.ofh.write("\nXXXXXX In add_alignment\n\n")
- # TODO: implement the draw_circos function for this.
- if len(self.contig_alignment) > 0:
- alignments = self.contig_alignment
- else:
- return
- self.doc.new_line()
- self.doc.new_header(level=2, title=self.alignment_title)
- self.doc.new_line()
- self.doc.new_header(level=3, title=self.snp_indel_title)
- Table_1 = [
- "Category",
- "Quantity",
- 'SNPs',
- '{:,}'.format(self.quast_mismatches),
- 'Small indels',
- '{:,}'.format(self.quast_indels)
- ]
+ 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')
+ quast_mismatches = int(float(quast_report.loc['# mismatches per 100 kbp', :][0]) * (float(quast_report.loc['Total length (>= 0 bp)', :][0]) / 100000.))
+ quast_indels = int(float(quast_report.loc['# indels per 100 kbp', :][0]) * (float(quast_report.loc['Total length (>= 0 bp)', :][0]) / 100000.))
+ self.doc.new_line()
+ self.doc.new_header(level=2, title=self.alignment_title)
+ self.doc.new_line()
+ self.doc.new_header(level=3, title=self.snp_indel_title)
+ Table_1 = [
+ "Category",
+ "Quantity",
+ 'SNPs',
+ '{:,}'.format(quast_mismatches),
+ 'Small indels',
+ '{:,}'.format(quast_indels)
+ ]
self.doc.new_table(columns=2, rows=3, text=Table_1, text_align='left')
self.doc.new_line('')
self.doc.new_line()
+ # TODO: self.alignment_notes is not currently populated.
if len(self.alignment_notes) > 0:
self.doc.new_header(level=3, title=self.alignment_notes_title)
for note in self.alignment_notes:
self.doc.new_line(note)
- for contig in alignments.index.tolist():
- contig_title = 'Alignment to %s' % contig
- image_png = alignments[contig]
- self.doc.new_line()
- self.doc.new_header(level=3, title=contig_title)
- self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(image_png)))
- self.doc.new_line('')
- self.doc.new_line()
+ if len(self.circos_files) > 0:
+ # Add circos PNG files.
+ for circos_file in self.circos_files:
+ contig = os.path.basename(circos_file)
+ contig_title = 'Alignment to %s' % contig
+ self.doc.new_line()
+ self.doc.new_header(level=3, title=contig_title)
+ self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(circos_file)))
+ self.doc.new_line('')
+ self.doc.new_line()
method = 'The genome assembly was aligned against the reference sequencing using dnadiff version %s.' % self.dnadiff_version
self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(pandas.Series(method))
@@ -643,7 +649,7 @@
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 %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 %s mpileup and %s.' % (self.samtools_version, self.varscan_version)
+ method = 'Mutations were identified using %s 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):
@@ -672,15 +678,6 @@
genome_insertions = pandas.DataFrame()
large_indels['Reference insertions'] = reference_insertions
large_indels['Query insertions'] = genome_insertions
- # TODO: we don't seem to be reporting snps and deletions for some reason...
- # Pull in the number of SNPs and small indels.
- try:
- snps = pandas.read_csv(filepath_or_buffer=self.dnadiff_snps_file, sep='\t', header=None)
- # TODO: the following is not used...
- # small_indels = snps.loc[(snps.iloc[:, 1] == '.') | (snps.iloc[:, 2] == '.'), :]
- snps = snps.loc[(snps.iloc[:, 1] != '.') & (snps.iloc[:, 2] != '.'), :]
- except Exception:
- snps = pandas.DataFrame()
# Pull in deletions.
try:
amr_deletions = pandas.read_csv(filepath_or_buffer=self.amr_deletion_file, sep='\t', header=None)
@@ -835,6 +832,7 @@
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('--circos_png_dir', action='store', dest='circos_png_dir', help='Directory of circos PNG files')
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')
@@ -854,6 +852,7 @@
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('--quast_report_file', action='store', dest='quast_report_file', help='Quast report tabular file')
parser.add_argument('--reference_insertions_file', action='store', dest='reference_insertions_file', help='Reference insertions BED 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')
@@ -865,6 +864,11 @@
for file_name in sorted(os.listdir(args.amr_matrix_png_dir)):
file_path = os.path.abspath(os.path.join(args.amr_matrix_png_dir, file_name))
amr_matrix_files.append(file_path)
+# Prepare the circos PNG files.
+circos_files = []
+for file_name in sorted(os.listdir(args.circos_png_dir)):
+ file_path = os.path.abspath(os.path.join(args.circos_png_dir, file_name))
+ circos_files.append(file_path)
# Prepare the features BED files.
feature_bed_files = []
for file_name in sorted(os.listdir(args.feature_bed_dir)):
@@ -888,6 +892,7 @@
args.assembly_name,
args.bedtools_version,
args.blastn_version,
+ circos_files,
args.compute_sequence_length_file,
args.contig_coverage_file,
args.dbkey,
@@ -907,6 +912,7 @@
mutation_regions_files,
args.pima_css,
args.plasmids_file,
+ args.quast_report_file,
args.reference_insertions_file,
args.samtools_version,
args.varscan_version)
diff -r 99613333fd1f -r f03c80bb22e9 pima_report.xml
--- a/pima_report.xml Fri Mar 10 16:35:16 2023 +0000
+++ b/pima_report.xml Thu Mar 16 14:42:13 2023 +0000
@@ -36,6 +36,7 @@
#end if
mkdir amr_matrix_png_dir &&
+mkdir circos_png_dir &&
mkdir feature_bed_dir &&
mkdir feature_png_dir &&
mkdir mutation_regions_dir &&
@@ -46,6 +47,11 @@
#set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
ln -s $i 'amr_matrix_png_dir/$identifier' &&
#end for
+#for $i in $circos_png:
+ #set file_name = $i.file_name
+ #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
+ ln -s $i 'circos_png_dir/$identifier' &&
+#end for
#for $i in $features_bed:
#set file_name = $i.file_name
#set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
@@ -74,6 +80,7 @@
#if str($blastn_features) not in ['None', '']:
--blastn_version '$blastn_version'
#end if
+--circos_png_dir 'circos_png_dir'
--compute_sequence_length_file '$compute_sequence_length_file'
--contig_coverage_file '$contig_coverage_file'
--dbkey '$aligned_sample.metadata.dbkey'
@@ -103,6 +110,7 @@
--mutation_regions_bed_file '$mutation_regions_bed_file'
--pima_css '${__tool_directory__}/pima.css'
--plasmids_file '$plasmids_file'
+--quast_report_file '$quast_report_file'
--reference_insertions_file '$reference_insertions_file'
#if str($samtools_pileup_file) not in ['None', '']:
--samtools_version '$samtools_version'
@@ -119,6 +127,7 @@
+
@@ -131,6 +140,7 @@
+