CHARLIE (Comprehensive High-throughput Analysis of Repeat Length, Interruptions and Expansions) is a suite of tools to analyse repeat size, filter FASTAs, find and quantify interruptions, and position interruptions within the repeat tract.
Usage: charlie [options]
Commands: info Show basic properties and statistics search Search for records containing a sequence filter Filter records by search sequence or repeat size repeats Measure repeat tract sizes inter Interruption tools
General Options: -h, --help Show this help message (use 'charlie -h' to see how use a specific command) -V, --version Show version '''
help_info=''' Usage: charlie info <input_file> [options]
Description: Displays properties of an input FASTX file. Shows basic file information, sequence length statistics, and quality/error statistics (FASTQ only).
It is assumed that FASTQ files are Sanger style using PHRED scores and an
ASCII offset of 33.
Required Arguments: <input_file> Path to input FASTX file
General Options: -h, --help Show this help message -V, --version Show version '''
help_search=''' Usage: charlie search <input_file> [options]
Description: Search sequences in records of an input FASTX file for an input sequence. Outputs total no. times the sequences appears (including multiple appearances in a single record), no. records in which the sequence appears, and the frequency of records containing the sequence.
By default the search method does not allow overlaps, meaning searching for
'CCC' in 'CCCCCC' would return 2 appearances. With overlaps optionally
enabled this same seach would return 4 appearances. Searching with overlaps
will increase runtime.
Required Arguments: <input_file> Path to input FASTX file Input search query sequence
Optional Arguments: -r, --revcomp Include reverse complement -o, --overlap Allow overlaps -q, --quiet Show only the number and frequency of records containing the sequence, displayed as NUMBER (FREQUENCY)
General Options: -h, --help Show this help message -V, --version Show version '''
help_filter=''' Usage: charlie filter <input_file> [options]
Description: Filter records of an input FASTX file by a query search sequence or repeat size. Filtering by repeat size only considers pure, uninterrupted repeat tracts.
Filtering by minimum and maximum repeat size simulatenously can be used to
obtain a range. Sequence filtering can be performed simultaneously to
repeat size filtering. If no filtering criteria options are selected, all
records will be output (this can be used alter the formatting of a file).
Required Arguments: <input_file> Path to input FASTX file
Optional Arguments: -s, --sequence Filter by input sequence -min, --minimum Filter by min. repeat size -max, --maximum Filter by max. repeat size -m, --motif <repeat_motif> Repeat motif (required if using -min or -max) -r, --revcomp Include reverse complement -w, --wrap Wrap sequence line width in output -o, --output Write output to new file (silences CLI output)
General Options: -h, --help Show this help message -V, --version Show version '''
help_repeats=''' Usage: charlie repeats <input_file> <repeat_motif> [options]
Description: Measure repeat tracts containing an input repeat motif (e.g. CAG) in records of an input FASTX file. Results are output to a csv and graph in the input file directory, and to command line interface (CLI) as a tab-delimited table.
Measurement assumes repeat tracts are pure and uninterrupted. Interrupted
repeat tracts will show as additional peaks in the graph. If an
interruption is of high frequency (near 1.0), the full repeat tract size
may be obscured.
For greater accuracy, or to measure interrupted repeat tracts, use:
https://github.com/DionLab/RepeatDetector
Required Arguments: <input_file> Path to input FASTX file <repeat_motif> Repeat motif/unit to search for (e.g. CAG)
Optional Arguments: -r, --revcomp Include reverse complement -s, --sort Sort results by no. records (descending) -q, --quiet Output to csv and graph only, no CLI output -c, --cli Output to CLI only, no csv or graph
General Options: -h, --help Show this help message -V, --version Show version '''
help_inter=''' Usage: charlie inter [options]
Description: The tools below are designed for the discovery and analysis of interruptions in repeat tracts.
Commands: find Search repeat tracts for possible interruptions position Determine modal position of a known interruption pattern [in development] correlation [in development]
General Options: -h, --help Show this help message (use 'charlie inter -h' to see how use a specific command) -V, --version Show version '''
help_inter_find=''' Usage: charlie inter find <input_file> <repeat_motif> [options]
Description: Search for possible interruptions of repeat tracts in an input FASTX file. Results are given as the number of records containing the interruption and the corresponding frequency.
Generates every possible interruption within a range (default 1-3 bases)
and searches record sequences for the interruption. In order to target the
repeat tract the search query is flanked with the repeat motif. For example,
to search for a CCG interruption in a CAG repeat tract, the search query
would be CAGCCGCAG.
If records contain sequences flanking the repeat tract sequences, some
queries may be present at high frequencies outisde the repeat tract. In
order to exclude these, specificity can be increased to increase the number
of repeat motifs in the search query. For example, at specificity 2 the
search query mentioned above would become CAGCAGCCGCAGCAG.
If records do not contain flanking sequences, specificity can be set to 0 to
increase accuracy.
This tool is optimised for shorter interruptions (<10 bases), increasing
maximum interruption size will increase runtime exponentially. The repeats
tool can be used to identify longer interruptions, see the repeats help for
more details. The filter tool can then be used to isolate long interruptions
for further review via the search tool or manually.
Required Arguments: <input_file> Path to input FASTX file <repeat_motif> Repeat motif/unit of repeat tract to be searched
Optional Arguments: -r, --revcomp Include reverse complement -t, --threshold Only show results above input record frequency (default: 0.05) -s, --specificity <num_motifs> Number of motifs either side of potential interruptions in search queries (default: 1) -min, --minimum Minimum interruption size (default: 1) -max, --maximum Maximum interruption size (default: 3) -v, --verbose Show full search queries in output -a, --appearances Also count the total appearances of interruptions within records (slower) -o, --output Export results to csv -q, --quiet (with --output enabled) csv output only, no CLI output
General Options: -h, --help Show this help message -V, --version Show version '''
help_inter_position=''' Usage: charlie inter position <input_file> <repeat_motif> [options]
Description: Determine the most common (modal) position of a known interruption within repeat tracts of an input FASTX file.
Generates histograms for the number of repeat motifs preceding and
following the interruption. The histograms are output to csv's and graphs.
Also determined and output to CLI:
- Percentage of records containing the interruption (greater than 0
preceding/following motifs)
- Modal number of preceding/following motifs
- Percentage of records with the modal numbers of motifs (of records
that contain the interruption)
- Modal interruption pattern, in format: (motif)P(inter)(motif)F
- Percentage of records with the modal interruption pattern (of records)
that contain the interruption)
One motif is placed on the opposite side of the interruption in all search
queries to ensure searches remain within the repeat tract.
Measurement assumes that the repeat tract either side of the interruption
is pure and contains no further interruptions. If multiple interruptions
are present, the full sequence spanning all interruptions must be given.
For example, if two CCG interruptions are present in a CAG repeat tract
with three CAG trinucleotides between them, the interruption sequence
should be input as CCGCAGCAGCAGCCG.
Keep in consideration that due to the assumption of pure repeat tracts,
each time the number of preceding or following motifs is increased, some
records may be omitted due to sequencing errors.
Required Arguments: <input_file> Path to input FASTX file <repeat_motif> Repeat motif/unit of repeat tract containing interruption Sequence of interruption to be positioned
Optional Arguments: -r, --revcomp Include reverse complement -v, --verbose Show top 10 result tables for preceding and following -g, --graphcrop Exclude the peak at 0 motifs from graphs (makes smaller peaks more visible) -q, --quiet Output to csv and graph only, no CLI output -c, --cli Output to CLI only, no csv or graph
General Options: -h, --help Show this help message -V, --version Show version '''
help_inter_pattern=''' Usage: charlie inter pattern <input_file> [options]
Description: [in development]
Required Arguments: [in developement]
General Options: -h, --help Show this help message -V, --version Show version '''
help_inter_correlation=''' Usage: charlie inter correlation <input_file> [options]
Description: [in development]
Required Arguments: [in developement]
General Options: -h, --help Show this help message -V, --version Show version '''
The other scripts in this folder have been used either to proess FASTA prior to CHARLIE or to compile the data obtained. See Heuchan et al for more information.