CustomQueryList

This program is a Python script used to reorganize and filter a query list that would be used in mScaffolder to scaffold a Flye assembly.

Overview

This tool is designed to take in a query list (format discussed below) of a Flye assembly, and use a configuration file to reorganize the order of contigs in the query list and output it to a new query list, as well as remove specified contigs from the query list. This outputted query list can then be used with mScaffolder to scaffold the original assembly that the query list was generated from.

Usage

Since this program assists with modifying query lists for use with mScaffolder, be sure to follow the mScaffolder workflow in order to prepare the assembly for scaffolding and generate the query list to be used as input here.

Input and ouput query list file formats

For the query list input of CustomQueryList, the contig ids must be in the format of "contig_{contig name}" or "scaffold_{sequence name}" in order to properly be processed. As well, the query list output will write the contig ids as "contig_{sequence name}".

Running the program

Usage of CustomQueryList is as follows:

python customQueryList.py [-h] -i <input> -o <output> -c <config>
	
	<input>
		input file in mScaffolder query list format (with contig ids of "contig_<contig name>" or "scaffold_<contig name>") 
		containing contig ids that will be processed
	<output>
		output file in mScaffolder query list format containing processed contig ids,
		excluding contigs that were specified to be filtered out.
	<config>
		input file in .config configuration file format (specified below)

options:
	-h, --help
		prints out the above usage statement

Configuration file format

The configuration file should be formatted as a .config file that specifies two possible operations that can be done on the assembly (each on a new line), and which sequences should be included in the operation.

The operations are as follows:

d: delete - all specified contigs name are removed from the main output file.
	format: d:<contig name>,<contig name>,...
m: move - all specified contigs are reorganized into order given, with the first contig remaining in its original position, and all following contigs being placed after the contig that immediately preceded it in the ordering.
        format: m:<contig name>-><contig name>-><contig name>...

Given the following example query list,

y tics
contig_1
contig_2
contig_3
contig_4
contig_5
contig_6
contig_7
contig_8
contig_9
contig_10

an example configuration file would be:

d:4,5
m:3->9->2
m:7->6

After running CustomQueryList with the example query list and configuration files as inputs, the outputted query list would be:

y tics
contig_1
contig_3
contig_9
contig_2
contig_7
contig_6
contig_8
contig_10

The configuration file does not need to include specifications for all operations, and you can have multiple lines for the same operations (for example, you can have multiple sets of reorder contigs, can specify contigs to be deleted over multiple lines).

Disclaimer

This tool was primarily used as an internal tool to process query lists that were used when scaffolding Flye assemblies with mScaffolder. Feel free to modify and/or build upon this code to fit your specific usage and needs.

License

This program is licensed under the Apache License Version 2.0. A copy of the Apache 2.0 license can be found here.