flowcraft.templates.process_abricate module

Purpose

This module is intended parse the results of the Abricate for one or more samples.

Expected input

The following variables are expected whether using NextFlow or the main() executor.

• abricate_files : Path to abricate output file.

  • e.g.: 'abr_resfinder.tsv'

Generated output

None

Code documentation

class flowcraft.templates.process_abricate.Abricate(fls)

Bases: object

Main parser for Abricate output files.

This class parses one or more output files from Abricate, usually from different databases. In addition to the parsing methods, it also provides a flexible method to filter and re-format the content of the abricate files.

Parameters:

fls : list

List of paths to Abricate output files.

Methods

get_filter(self, \*args, \*\*kwargs)	Wrapper of the iter_filter method that returns a list with results
iter_filter(self, filters[, databases, …])	General purpose filter iterator.
parse_files(self, fls)	Public method for parsing abricate output files.

storage = None

dic: Main storage of Abricate’s file content. Each entry corresponds to a single line and contains the keys:

- ``log_file``: Name of the summary log file containing abricate
  results
- ``infile``: Input file of Abricate.
- ``reference``: Reference of the query sequence.
- ``seq_range``: Range of the query sequence in the database
 sequence.
- ``gene``: AMR gene name.
- ``accession``: The genomic source of the sequence.
- ``database``: The database the sequence came from.
- ``coverage``: Proportion of gene covered.
- ``identity``: Proportion of exact nucleotide matches.

parse_files(self, fls)

Public method for parsing abricate output files.

This method is called at at class instantiation for the provided output files. Additional abricate output files can be added using this method after the class instantiation.

Parameters:

fls : list

List of paths to Abricate files

iter_filter(self, filters, databases=None, fields=None, filter_behavior='and')

General purpose filter iterator.

This general filter iterator allows the filtering of entries based on one or more custom filters. These filters must contain an entry of the storage attribute, a comparison operator, and the test value. For example, to filter out entries with coverage below 80:

my_filter = ["coverage", ">=", 80]

Filters should always be provide as a list of lists:

iter_filter([["coverage", ">=", 80]])
# or
my_filters = [["coverage", ">=", 80],
              ["identity", ">=", 50]]

iter_filter(my_filters)

As a convenience, a list of the desired databases can be directly specified using the database argument, which will only report entries for the specified databases:

iter_filter(my_filters, databases=["plasmidfinder"])

By default, this method will yield the complete entry record. However, the returned filters can be specified using the fields option:

iter_filter(my_filters, fields=["reference", "coverage"])

Parameters:

filters : list

List of lists with the custom filter. Each list should have three elements. (1) the key from the entry to be compared; (2) the comparison operator; (3) the test value. Example:

[["identity", ">", 80]].

databases : list

List of databases that should be reported.

fields : list

List of fields from each individual entry that are yielded.

filter_behavior : str

options: 'and' 'or' Sets the behaviour of the filters, if multiple filters have been provided. By default it is set to 'and', which means that an entry has to pass all filters. It can be set to 'or', in which case one one of the filters has to pass.

Yields:

dic : dict

Dictionary object containing a Abricate.storage entry that passed the filters.

get_filter(self, *args, **kwargs)

Wrapper of the iter_filter method that returns a list with results

It should be called exactly as in the iter_filter

Returns:

_ : list

List of dictionary entries that passed the filters in the iter_filter method.

See also

iter_filter

class flowcraft.templates.process_abricate.AbricateReport(*args, **kwargs)

Bases: flowcraft.templates.process_abricate.Abricate

Report generator for single Abricate output files

This class is intended to parse an Abricate output file from a single sample and database and generates a JSON report for the report webpage.

Parameters:

fls : list

List of paths to Abricate output files.

database : (optional) str

Name of the database for the current report. If not provided, it will be inferred based on the first entry of the Abricate file.

Methods

get_filter(self, \*args, \*\*kwargs)	Wrapper of the iter_filter method that returns a list with results
get_plot_data(self)	Generates the JSON report to plot the gene boxes
get_table_data(self)
iter_filter(self, filters[, databases, …])	General purpose filter iterator.
parse_files(self, fls)	Public method for parsing abricate output files.
write_report_data(self)	Writes the JSON report to a json file

get_plot_data(self)

Generates the JSON report to plot the gene boxes

Following the convention of the reports platform, this method returns a list of JSON/dict objects with the information about each entry in the abricate file. The information contained in this JSON is:

{contig_id: <str>,
 seqRange: [<int>, <int>],
 gene: <str>,
 accession: <str>,
 coverage: <float>,
 identity: <float>
 }

Note that the seqRange entry contains the position in the corresponding contig, not the absolute position in the whole assembly.

Returns:

json_dic : list

List of JSON/dict objects with the report data.

get_table_data(self)

write_report_data(self)

Writes the JSON report to a json file