# HG changeset patch
# User greg
# Date 1678205114 0
# Node ID 67d0939b56b06d9fe44a536ef6d3772f00f69745
# Parent 0a558f444c98160e03aed31d7dc157fd9301a9de
Uploaded
diff -r 0a558f444c98 -r 67d0939b56b0 pima_report.py
--- a/pima_report.py Fri Mar 03 22:06:23 2023 +0000
+++ b/pima_report.py Tue Mar 07 16:05:14 2023 +0000
@@ -15,37 +15,57 @@
class PimaReport:
- def __init__(self, analysis_name=None, assembly_fasta_file=None, assembly_name=None, feature_bed_files=None, feature_png_files=None,
- contig_coverage_file=None, dbkey=None, gzipped=None, illumina_fastq_file=None, mutation_regions_bed_file=None,
- mutation_regions_tsv_files=None, pima_css=None):
+ def __init__(self, analysis_name=None, amr_deletions_file=None, amr_matrix_files=None, assembly_fasta_file=None,
+ assembly_name=None, compute_sequence_length_file=None, contig_coverage_file=None, dbkey=None,
+ dnadiff_snps_file=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,
+ mutation_regions_bed_file=None, mutation_regions_tsv_files=None, pima_css=None, plasmids_file=None,
+ reference_insertions_file=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("assembly_fasta_file: %s\n" % str(assembly_fasta_file))
self.ofh.write("assembly_name: %s\n" % str(assembly_name))
+ 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("feature_bed_files: %s\n" % str(feature_bed_files))
self.ofh.write("feature_png_files: %s\n" % str(feature_png_files))
- self.ofh.write("contig_coverage_file: %s\n" % str(contig_coverage_file))
- self.ofh.write("dbkey: %s\n" % str(dbkey))
+ self.ofh.write("flye_assembly_info_file: %s\n" % str(flye_assembly_info_file))
+ self.ofh.write("flye_version: %s\n" % str(flye_version))
self.ofh.write("gzipped: %s\n" % str(gzipped))
+ self.ofh.write("genome_insertions_file: %s\n" % str(genome_insertions_file))
self.ofh.write("illumina_fastq_file: %s\n" % str(illumina_fastq_file))
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))
# General
self.doc = None
self.report_md = 'pima_report.md'
# Inputs
+ self.amr_deletions_file = amr_deletions_file
+ self.amr_matrix_files = amr_matrix_files
self.analysis_name = analysis_name
self.assembly_fasta_file = assembly_fasta_file
self.assembly_name = assembly_name
+ 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.feature_bed_files = feature_bed_files
self.feature_png_files = feature_png_files
- self.contig_coverage_file = contig_coverage_file
- self.dbkey = dbkey
+ self.flye_assembly_info_file = flye_assembly_info_file
+ self.flye_version = flye_version
self.gzipped = gzipped
+ self.genome_insertions_file = genome_insertions_file
self.illumina_fastq_file = illumina_fastq_file
self.mutation_regions_bed_file = mutation_regions_bed_file
self.mutation_regions_tsv_files = mutation_regions_tsv_files
@@ -54,6 +74,9 @@
self.ont_n50 = None
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
# Titles
self.alignment_title = 'Comparison with reference'
@@ -73,9 +96,9 @@
self.mutation_title = 'Mutations found in the sample'
self.mutation_methods_title = 'Mutation screening'
self.plasmid_methods_title = 'Plasmid annotation'
+ self.plasmid_title = 'Plasmid annotation'
self.reference_methods_title = 'Reference comparison'
self.snp_indel_title = 'SNPs and small indels'
- #self.summary_title = 'Summary'
self.summary_title = 'Analysis of %s' % analysis_name
# Methods
@@ -98,7 +121,6 @@
# Values
self.assembly_size = 0
self.contig_info = None
- self.did_flye_ont_fastq = False
self.did_medaka_ont_assembly = False
self.feature_hits = pandas.Series(dtype='float64')
self.illumina_length_mean = 0
@@ -106,6 +128,11 @@
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
@@ -139,6 +166,22 @@
self.contig_info[self.read_type] = pandas.read_csv(self.contig_coverage_file, header=None, index_col=None, sep='\t').sort_values(1, axis=0, ascending=False)
self.contig_info[self.read_type].columns = ['contig', 'size', 'coverage']
self.mean_coverage = (self.contig_info[self.read_type].iloc[:, 1] * self.contig_info[self.read_type].iloc[:, 2]).sum() / self.contig_info[self.read_type].iloc[:, 1].sum()
+ if self.mean_coverage <= self.ont_coverage_min:
+ warning = '%s mean coverage ({:.0f}X) is less than the recommended minimum ({:.0f}X).'.format(self.mean_coverage, self.ont_coverage_min) % self.read_type
+ self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
+ # Report if some contigs have low coverage.
+ low_coverage = self.contig_info[self.read_type].loc[self.contig_info[self.read_type]['coverage'] < self.ont_coverage_min, :]
+ if low_coverage.shape[0] >= 0:
+ for contig_i in range(low_coverage.shape[0]):
+ warning = '%s coverage of {:s} ({:.0f}X) is less than the recommended minimum ({:.0f}X).'.format(low_coverage.iloc[contig_i, 0], low_coverage.iloc[contig_i, 2], self.ont_coverage_min) % self.read_type
+ self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
+ # See if some contigs have anolously low coverage.
+ fold_coverage = self.contig_info[self.read_type]['coverage'] / self.mean_coverage
+ low_coverage = self.contig_info[self.read_type].loc[fold_coverage < 1 / 5, :]
+ if low_coverage.shape[0] >= 0 :
+ for contig_i in range(low_coverage.shape[0]):
+ warning = '%s coverage of {:s} ({:.0f}X) is less than 1/5 the mean coverage ({:.0f}X).'.format(low_coverage.iloc[contig_i, 0], low_coverage.iloc[contig_i, 2], self.mean_coverage) % self.read_type
+ self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
def load_fasta(self, fasta):
sequence = pandas.Series(dtype=object)
@@ -185,7 +228,6 @@
self.illumina_bases = self.format_kmg(self.illumina_bases, decimals=1)
def start_doc(self):
- #header_text = 'Analysis of %s' % self.analysis_name
self.doc = MdUtils(file_name=self.report_md, title='')
def add_run_information(self):
@@ -256,6 +298,20 @@
]
self.doc.new_table(columns=2, rows=4, text=Table_List, text_align='left')
+ def evaluate_assembly(self) :
+ assembly_info = pandas.read_csv(self.compute_sequence_length_file, sep='\t', header=None)
+ assembly_info.columns = ['contig', 'length']
+ self.contig_sizes = assembly_info
+ # Take a look at the number of contigs, their sizes,
+ # and circularity. Warn if things don't look good.
+ if assembly_info.shape[0] > 4:
+ warning = 'Assembly produced {:d} contigs, more than ususally expected; assembly may be fragmented'.format(assembly_info.shape[0])
+ self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
+ small_contigs = assembly_info.loc[assembly_info['length'] <= 3000, :]
+ if small_contigs.shape[0] > 0:
+ warning = 'Assembly produced {:d} small contigs ({:s}); assembly may include spurious sequences.'.format(small_contigs.shape[0], ', '.join(small_contigs['contig']))
+ 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:
@@ -291,15 +347,17 @@
if result[1] == '0':
self.error_out('No ONT reads found')
ont_n50, ont_read_count, ont_raw_bases = [int(i) for i in result]
-
command = ' '.join([opener,
fastq_file,
'| awk \'{getline;print length($0);getline;getline;}\''])
result = self.run_command(command)
result = list(filter(lambda x: x != '', result))
- ont_read_lengths = [int(i) for i in result]
-
- return ([ont_n50, ont_read_count, ont_raw_bases, ont_read_lengths])
+ # TODO: the following are not yet used...
+ # ont_read_lengths = [int(i) for i in result]
+ # ont_bases = self.format_kmg(ont_raw_bases, decimals=1)
+ if ont_n50 <= self.ont_n50_min:
+ warning = 'ONT N50 (%s) is less than the recommended minimum (%s)' % (str(ont_n50), str(self.ont_n50_min))
+ self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
def wordwrap_markdown(self, string):
if string:
@@ -347,8 +405,8 @@
self.doc.new_line('')
self.doc.new_line()
self.doc.new_header(2, self.assembly_notes_title)
- #for note in self.analysis.assembly_notes:
- # self.doc.new_line(note)
+ for note in self.assembly_notes:
+ self.doc.new_line(note)
def add_contamination(self):
self.ofh.write("\nXXXXXX In add_contamination\n\n")
@@ -384,11 +442,9 @@
"Category",
"Quantity",
'SNPs',
- #'{:,}'.format(self.analysis.quast_mismatches),
- 'NA'
+ '{:,}'.format(self.quast_mismatches),
'Small indels',
- #'{:,}'.format(self.analysis.quast_indels)
- 'NA'
+ '{:,}'.format(self.quast_indels)
]
self.doc.new_table(columns=2, rows=3, text=Table_1, text_align='left')
self.doc.new_line('')
@@ -444,12 +500,17 @@
feature = contig_features.iloc[i, :].copy(deep=True)
self.ofh.write("feature: %s\n" % str(feature))
feature[4] = '{:.3f}'.format(feature[4])
- Table_List = Table_List + feature[1:].values.tolist()
+ # FIXME: Uncommenting the following line (which is
+ # https://github.com/appliedbinf/pima_md/blob/main/MarkdownReport.py#L317)
+ # will cause the job to fail with this exception:
+ # ValueError: columns * rows is not equal to text length
+ # 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.doc.new_table(columns=7, rows=row_count, text=Table_List, text_align='left')
+ 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 blastn.'
bedtools_version = 'Feature hits were clustered using bedtools and the highest scoring hit for each cluster was reported.'
method = '%s %s' % (blastn_version, bedtools_version)
@@ -469,11 +530,34 @@
self.ofh.write("\nXXXXXX In add_mutations\n\n")
if len(self.mutation_regions_tsv_files) == 0:
return
- try:
+ try :
mutation_regions = pandas.read_csv(self.mutation_regions_bed_file, sep='\t', header=0, index_col=False)
except Exception:
# Likely an empty file.
return
+ # TODO: this is the only place where reference_genome is used,
+ # so I'm commenting it out for now. We need to confirm if these
+ # errors that require the reference genmoe being passed are necessary.
+ # If so, we'll need to implement data tables in this tool.
+ # Make sure that the positions in the BED file fall within
+ # the chromosomes provided in the reference sequence.
+ """
+ for mutation_region in range(mutation_regions.shape[0]):
+ mutation_region = mutation_regions.iloc[mutation_region, :]
+ if not (mutation_region[0] in self.reference_genome):
+ self.ofh.write("\nMutation region: %s not found in reference genome.\n" % ' '.join(mutation_region.astype(str)))
+ continue
+ if not isinstance(mutation_region[1], int):
+ self.ofh.write("\nNon-integer found in mutation region start (column 2): %s.\n" % str(mutation_region[1]))
+ break
+ elif not isinstance(mutation_region[2], int):
+ self.ofh.write("\nNon-integer found in mutation region start (column 3): %s.\n" % str(mutation_region[2]))
+ break
+ if mutation_region[1] <= 0 or mutation_region[2] <= 0:
+ self.ofh.write("\nMutation region %s starts before the reference sequence.\n" % ' '.join(mutation_region.astype(str)))
+ if mutation_region[1] > len(self.reference_genome[mutation_region[0]].seq) or mutation_region[2] > len(self.reference_genome[mutation_region[0]].seq):
+ self.ofh.write("\nMutation region %s ends after the reference sequence.\n" % ' '.join(mutation_region.astype(str)))
+ """
amr_mutations = pandas.Series(dtype=object)
for region_i in range(mutation_regions.shape[0]):
region = mutation_regions.iloc[region_i, :]
@@ -483,13 +567,13 @@
if region_mutations_tsv_name not in self.mutation_regions_tsv_files:
continue
region_mutations_tsv = self.mutation_regions_tsv_files[region_mutations_tsv_name]
- try:
+ try :
region_mutations = pandas.read_csv(region_mutations_tsv, sep='\t', header=0, index_col=False)
except Exception:
region_mutations = pandas.DataFrame()
if region_mutations.shape[0] == 0:
continue
- # Figure out what kind of mutations are in this region
+ # Figure out what kind of mutations are in this region.
region_mutation_types = pandas.Series(['snp'] * region_mutations.shape[0], name='TYPE', index=region_mutations.index)
region_mutation_types[region_mutations['REF'].str.len() != region_mutations['ALT'].str.len()] = 'small-indel'
region_mutation_drugs = pandas.Series(region['drug'] * region_mutations.shape[0], name='DRUG', index=region_mutations.index)
@@ -521,78 +605,85 @@
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 not getattr(self.analysis, 'did_draw_amr_matrix', False):
- # return
- #amr_matrix_png = self.analysis.amr_matrix_png
- #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.')
- #self.doc.new_line(
- # self.doc.new_inline_image(
- # text='AMR genes and mutations with their corresponding drugs',
- # path=amr_matrix_png
- # )
- #)
- pass
+ 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')
+ 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)))
def add_large_indels(self):
self.ofh.write("\nXXXXXX In add_large_indels\n\n")
- # Make sure we looked for mutations
- #if len(self.analysis.large_indels) == 0:
- # return
- #large_indels = self.analysis.large_indels
- #self.doc.new_line()
- #self.doc.new_header(level=2, title=self.large_indel_title)
- #for genome in ['Reference insertions', 'Query insertions']:
- # genome_indels = large_indels[genome].copy()
- # self.doc.new_line()
- # self.doc.new_header(level=3, title=genome)
- # if (genome_indels.shape[0] == 0):
- # continue
- # genome_indels.iloc[:, 1] = genome_indels.iloc[:, 1].apply(lambda x: '{:,}'.format(x))
- # genome_indels.iloc[:, 2] = genome_indels.iloc[:, 2].apply(lambda x: '{:,}'.format(x))
- # genome_indels.iloc[:, 3] = genome_indels.iloc[:, 3].apply(lambda x: '{:,}'.format(x))
- # Table_List = [
- # 'Reference contig', 'Start', 'Stop', 'Size (bp)'
- # ]
- # for i in range(genome_indels.shape[0]):
- # 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.'
- #self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(
- # pandas.Series(method))
- #self.doc.new_line()
- #self.doc.new_line('')
- #self.doc.new_line()
- pass
+ large_indels = pandas.Series(dtype='float64')
+ # Pull in insertions.
+ try:
+ reference_insertions = pandas.read_csv(filepath_or_buffer=self.reference_insertions_file, sep='\t', header=None)
+ except Exception:
+ reference_insertions = pandas.DataFrame()
+ try:
+ genome_insertions = pandas.read_csv(filepath_or_buffer=self.genome_insertions_file, sep='\t', header=None)
+ except Exception:
+ 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)
+ except Exception:
+ amr_deletions = pandas.DataFrame()
+ if amr_deletions.shape[0] > 0:
+ amr_deletions.columns = ['contig', 'start', 'stop', 'name', 'type', 'drug', 'note']
+ amr_deletions = amr_deletions.loc[amr_deletions['type'].isin(['large-deletion', 'any']), :]
+ self.doc.new_line()
+ self.doc.new_header(level=2, title=self.large_indel_title)
+ for genome in ['Reference insertions', 'Query insertions']:
+ genome_indels = large_indels[genome].copy()
+ self.doc.new_line()
+ self.doc.new_header(level=3, title=genome)
+ if (genome_indels.shape[0] == 0):
+ continue
+ genome_indels.iloc[:, 1] = genome_indels.iloc[:, 1].apply(lambda x: '{:,}'.format(x))
+ genome_indels.iloc[:, 2] = genome_indels.iloc[:, 2].apply(lambda x: '{:,}'.format(x))
+ genome_indels.iloc[:, 3] = genome_indels.iloc[:, 3].apply(lambda x: '{:,}'.format(x))
+ Table_List = [
+ 'Reference contig', 'Start', 'Stop', 'Size (bp)'
+ ]
+ for i in range(genome_indels.shape[0]):
+ 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.'
+ self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(pandas.Series(method))
+ self.doc.new_line()
+ self.doc.new_line('')
+ self.doc.new_line()
def add_plasmids(self):
- self.ofh.write("\nXXXXXX In add_plasmids\n\n")
- """
- if not getattr(self.analysis, 'did_call_plasmids', False):
- return
- # Make sure we looked for mutations
- #plasmids = self.analysis.plasmids
- if plasmids is None:
+ try :
+ plasmids = pandas.read_csv(filepath_or_buffer=self.plasmids_file, sep='\t', header=0)
+ except Exception:
return
plasmids = plasmids.copy()
self.doc.new_line()
- #self.doc.new_header(level=2, title=self.analysis.plasmid_title)
+ self.doc.new_header(level=2, title=self.plasmid_title)
if (plasmids.shape[0] == 0):
self.doc.new_line('None')
return
plasmids.iloc[:, 3] = plasmids.iloc[:, 3].apply(lambda x: '{:,}'.format(x))
plasmids.iloc[:, 4] = plasmids.iloc[:, 4].apply(lambda x: '{:,}'.format(x))
plasmids.iloc[:, 5] = plasmids.iloc[:, 5].apply(lambda x: '{:,}'.format(x))
- Table_List = [
- 'Genome contig',
- 'Plasmid hit',
- 'Plasmid acc.',
- 'Contig size',
- 'Aliged',
- 'Plasmid size'
- ]
+ Table_List = ['Genome contig', 'Plasmid hit', 'Plasmid acc.', 'Contig size', 'Aliged', 'Plasmid size']
for i in range(plasmids.shape[0]):
Table_List = Table_List + plasmids.iloc[i, 0:6].values.tolist()
row_count = int(len(Table_List) / 6)
@@ -603,8 +694,6 @@
self.methods[self.plasmid_methods_title] = self.methods[self.plasmid_methods_title].append(pandas.Series(method))
method = 'Plasmid-to-genome hits were resolved using the pChunks algorithm.'
self.methods[self.plasmid_methods_title] = self.methods[self.plasmid_methods_title].append(pandas.Series(method))
- """
- pass
def add_methods(self):
self.ofh.write("\nXXXXXX In add_methods\n\n")
@@ -614,7 +703,6 @@
return
self.doc.new_line()
self.doc.new_header(level=2, title=self.methods_title)
-
for methods_section in self.methods.index.tolist():
if self.methods[methods_section] is None or len(self.methods[methods_section]) == 0:
continue
@@ -639,15 +727,25 @@
methods += ['ONT reads were demultiplexed and trimmed using qcat']
self.methods[self.basecalling_methods_title] = pandas.Series(methods)
self.add_illumina_library_information()
+ self.add_contig_info()
+ self.evaluate_assembly()
self.add_assembly_information()
- self.add_contig_info()
- self.add_assembly_notes()
- if self.did_flye_ont_fastq:
- method = 'ONT reads were assembled using Flye.'
+ if self.flye_assembly_info_file is not None:
+ method = 'ONT reads were assembled using %s' % self.flye_version
self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method))
+ # Pull in the assembly summary and look at the coverage.
+ assembly_info = pandas.read_csv(self.flye_assembly_info_file, header=0, index_col=0, sep='\t')
+ # Look for non-circular contigs.
+ open_contigs = assembly_info.loc[assembly_info['circ.'] == 'N', :]
+ if open_contigs.shape[0] > 0:
+ open_contig_ids = open_contigs.index.values
+ warning = 'Flye reported {:d} open contigs ({:s}); assembly may be incomplete.'.format(open_contigs.shape[0], ', '.join(open_contig_ids))
+ self.assembly_notes = self.assembly_notes.append(pandas.Series(warning))
if self.did_medaka_ont_assembly:
method = 'the genome assembly was polished using ont reads and medaka.'
self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.series(method))
+ self.info_ont_fastq(self.illumina_fastq_file)
+ self.add_assembly_notes()
def make_tex(self):
self.doc.new_table_of_contents(table_title='detailed run information', depth=2, marker="tableofcontents")
@@ -666,9 +764,9 @@
self.add_features()
self.add_feature_plots()
self.add_mutations()
- # TODO stuff working to here...
self.add_large_indels()
self.add_plasmids()
+ # TODO stuff working to here...
self.add_amr_matrix()
# self.add_snps()
self.add_methods()
@@ -687,21 +785,36 @@
parser = argparse.ArgumentParser()
+parser.add_argument('--amr_deletions_file', action='store', dest='amr_deletions_file', help='AMR deletions BED file')
+parser.add_argument('--amr_matrix_png_dir', action='store', dest='amr_matrix_png_dir', help='Directory of AMR matrix PNG files')
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('--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('--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('--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')
+parser.add_argument('--flye_assembly_info_file', action='store', dest='flye_assembly_info_file', default=None, help='Flye assembly info tabular file')
+parser.add_argument('--flye_version', action='store', dest='flye_version', default=None, help='Flye version string')
+parser.add_argument('--genome_insertions_file', action='store', dest='genome_insertions_file', help='Genome insertions BED file')
parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Input sample is gzipped')
parser.add_argument('--illumina_fastq_file', action='store', dest='illumina_fastq_file', help='Input sample')
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')
args = parser.parse_args()
+# Prepare the AMR matrix PNG files.
+amr_matrix_files = []
+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 features BED files.
feature_bed_files = []
for file_name in sorted(os.listdir(args.feature_bed_dir)):
@@ -719,15 +832,24 @@
mutation_regions_files.append(file_path)
markdown_report = PimaReport(args.analysis_name,
+ args.amr_deletions_file,
+ amr_matrix_files,
args.assembly_fasta_file,
args.assembly_name,
+ args.compute_sequence_length_file,
+ args.contig_coverage_file,
+ args.dbkey,
+ args.dnadiff_snps_file,
feature_bed_files,
feature_png_files,
- args.contig_coverage_file,
- args.dbkey,
+ args.flye_assembly_info_file,
+ args.flye_version,
+ args.genome_insertions_file,
args.gzipped,
args.illumina_fastq_file,
args.mutation_regions_bed_file,
mutation_regions_files,
- args.pima_css)
+ args.pima_css,
+ args.plasmids_file,
+ args.reference_insertions_file)
markdown_report.make_report()
diff -r 0a558f444c98 -r 67d0939b56b0 pima_report.xml
--- a/pima_report.xml Fri Mar 03 22:06:23 2023 +0000
+++ b/pima_report.xml Tue Mar 07 16:05:14 2023 +0000
@@ -9,12 +9,22 @@
#set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
#set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
+#if str($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
+mkdir amr_matrix_png_dir &&
mkdir feature_bed_dir &&
mkdir feature_png_dir &&
mkdir mutation_regions_dir &&
touch 'pima_report.pdf' &&
+#for $i in $amr_matrices_png:
+ #set file_name = $i.file_name
+ #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
+ ln -s $i 'amr_matrix_png_dir/$identifier' &&
+#end for
#for $i in $features_bed:
#set file_name = $i.file_name
#set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
@@ -32,13 +42,22 @@
#end for
python '${__tool_directory__}/pima_report.py'
+--amr_matrix_png_dir 'amr_matrix_png_dir'
+--amr_deletions_file '$amr_deletions_file'
--analysis_name '$analysis_name'
--assembly_fasta_file '$assembly_fasta_file'
--assembly_name '$assembly_name'
+--compute_sequence_length_file '$compute_sequence_length_file'
--contig_coverage_file '$contig_coverage_file'
--dbkey '$aligned_sample.metadata.dbkey'
+--dnadiff_snps_file '$dnadiff_snps_file'
--feature_bed_dir 'feature_bed_dir'
--feature_png_dir 'feature_png_dir'
+#if str($flye_assembly_info_file) not in ['None', '']:
+ --flye_assembly_info_file '$flye_assembly_info_file'
+ --flye_version '$flye_version'
+#end if
+--genome_insertions_file '$genome_insertions_file'
#if $illumina_fastq_file.ext.endswith(".gz"):
--gzipped
#end if
@@ -46,17 +65,27 @@
--mutation_regions_dir 'mutation_regions_dir'
--mutation_regions_bed_file '$mutation_regions_bed_file'
--pima_css '${__tool_directory__}/pima.css'
+--plasmids_file '$plasmids_file'
+--reference_insertions_file '$reference_insertions_file'
&& mv 'pima_report.pdf' '$output'
]]>
+
+
+
+
+
-
+
+
+
+