assemblerflow.templates.mapping2json module

Purpose

This module is intended to generate a json output for mapping results that can be imported in pATLAS.

Expected input

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

• depth_file : String with the name of the mash screen output file.

  • e.g.: 'samtoolsDepthOutput_sampleA.txt'

• json_dict : the file that contains the dictionary with keys and values for

  accessions and their respective lengths.

  • e.g.: 'reads_sample_result_length.json'

• cutoff : The cutoff used to trim the unwanted matches for the minimum

  coverage results from mapping. This value may range between 0 and 1.

  • e.g.: 0.6

Code documentation

assemblerflow.templates.mapping2json.depthfilereader(depth_file, plasmid_length, cutoff)

Function that parse samtools depth file and creates 3 dictionaries that will be useful to make the outputs of this script, both the tabular file and the json file that may be imported by pATLAS

Parameters:

depth_file: str

the path to depth file for each sample

plasmid_length: dict

a dictionary that stores length of all plasmids in fasta given as input

cutoff: str

the cutoff used to trim the unwanted matches for the minimum coverage results from mapping. This is then converted into a float within this function in order to compare with the value returned from the perc_value_per_ref.

Returns:

percentage_basescovered: dict

stores the percentage of the total sequence of a reference/accession (plasmid) in a dictionary