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commands.md

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Commands and Options

  • reform:
    Convert basecaller's move table to ss string format.
  • realign:
    Realign signal to reference using cigar string and the move table.
  • plot:
    Plot read/reference - signal alignments.
  • plot_pileup:
    Plot a reference - signal alignment pileup.
  • plot_tracks:
    Plot multiple reference - signal alignment pileup tracks.
  • calculate_offsets:
    A utility program to calculate the most significant base index given a kmer model or a read - signal alignment.
  • metric:
    A utility program to calculate some statistics of the signal alignment.

reform

squigualiser reform [OPTIONS] -c --bam basecall_moves.sam -o reform.paf
squigualiser reform [OPTIONS] --bam basecall_moves.sam -o reform.tsv

Convert basecaller's move table to ss string format. For more information refer reform.

  • --bam FILE:
    The basecaller's move table output in sam or bam format. Guppy outputs multiple sam/bam files. These files have to be merged to create a single sam/bam file.
  • -o, --output FILE :
    Specifies name/location of the output file. A valid relative or absolute path can be provided. Data will be overwritten. The extension should be either .tsv or .paf.
  • -k, --kmer_length INT:
    (optional) kmer length to consider for the calculation.
  • -m, --sig_move_offset INT:
    (optional) signal move offset to consider for the calculation.
  • -c:
    (optional) write move table in paf format. [default is tsv]
  • --rna:
    (optional) Specify if RNA reads are used. By default, only DNA is accepted [default value: false]. The tool will not error out if the data is RNA but if the user failed to specify it. It will still generate an incorrect output.
  • --profile STR:
    (optional) This is used to determine -k and -m values using preset values. The available profiles can be listed using --list_profile
  • --list_profile:
    (optional) Print the available profiles and exit.

realign

squigualiser realign [OPTIONS] -c --bam minimap2.sam --paf reform_output.paf -o realign_output.paf
squigualiser realign [OPTIONS] -c --bam minimap2.bam --paf reform_output.paf -o realign_output.paf
squigualiser realign [OPTIONS] --bam minimap2.bam --paf reform_output.paf -o realign_output.sam
squigualiser realign [OPTIONS] --bam minimap2.bam --paf reform_output.paf -o realign_output.bam

Realign signal to reference using cigar string and the move table. For more information refer realign.

  • --paf FILE:
    The read-signal alignment file generated using reform with -c option.
  • --bam FILE:
    The read-reference alignment sam/bam file containing cigar strings (minimap2 sam output).
  • -o, --output FILE :
    Specifies name/location of the output file. A valid relative or absolute path can be provided. Data will be overwritten. The extension should be .sam, .bam, or .paf.
  • -c:
    (optional) write move table in paf format. [default is sam or bam depending on the extension provided]
  • --rna:
    (optional) Specify if RNA reads are used. By default, only DNA is accepted [default value: false].

plot

squigualiser plot [OPTIONS] -f reads.fasta -s reads.slow5 -a reform.paf -o output_dir
squigualiser plot [OPTIONS] -f reads.fastq -s reads.slow5 -a reform.paf -o output_dir
squigualiser plot [OPTIONS] -f reads.fasta -s reads.slow5 -a realign.sam -o output_dir
squigualiser plot [OPTIONS] -f reads.fasta -s reads.slow5 -a realign.paf.gz -o output_dir

Plot read/reference - signal alignments.

  • -f, --file FILE:
    The sequence file in fasta/fa/fastq/fq/fq.gz format.
  • -r, --read_id STR (optional) Plot only the read with the read id specified.
  • -s, --slow5 FILE Path to slow5 file containing raw signals.
  • -a, --alignment FILE For read-signal alignment plots provide the path to .paf file generated using reform. For reference-signal alignment plots provide the .sam/.bam or .paf.gz file (generated using realgin or f5c eventalign).
  • --region STR [start-end] 1-based closed interval region to plot. For read-signal alignment eg:100-200. For reference-signal alignment eg: chr1:6811428-6811467 or chr1:6,811,428-6,811,467.
  • -o, --output_dir DIR :
    Specifies name/location of the output directory. A valid relative or absolute path can be provided. Data will be overwritten but the directory will not be recreated.
  • --tag_name STR (optional) A tag name to easily identify the plot.
  • -k, --kmer_length INT (optional) kmer length to consider for the base shift calculation and plotting.
  • --plot_reverse (optional) Plot only the reverse mapped reads [default value: false].
  • --rna (optional) Specify if RNA reads are used. By default, only DNA is accepted [default value: false].
  • --base_limit INT (optional) Maximum number of bases to plot.
  • --sig_ref (optional) Plot signal to reference mapping. Can be mostly discarded. Act as a flag to avoid ploting reference-signal alignment using a .paf alignment file [default value: false].
  • --fixed_width (optional) Plot with fixed base width. By default, the base widht is stretched to have equal distance between the sample points. By activating this flag, sample points of a base will be squeezed to a fixed width. [default value: false]
  • --sig_scale (optional) Plot the scaled signal. By default, the signal is not scaled but converted to pA values. Supported scalings are: [medmad, znorm, scaledpA]. medmad is median absolute deviation scaling.
    znorm is zscore normalization scaling. scaledpA uses sc and sh tags to scale the raw signal to the pore model. The implementation of each method can be found at src/plot_utils.py/scale_signal()
  • --no_pa (optional) Do not convert the signal to pA levels. By default, the raw signal is converted to pA levels [default value: false].
  • --loose_bound (optional) Also plot alignments not completely within the specified region but at least part is [default value: false].
  • --point_size INT (optional) Radius of the signal point drawn in the plot [default value: 0.5].
  • --base_width INT (optional) The base width when plotting with fixed base width [default value: 10].
  • --base_shift INT (optional) The number of bases to shift to align fist signal move [default value: 0]. More information on this can be found at here
  • --auto (optional) Calculate and automatically set the base shift. [default value: false]
  • --profile STR:
    (optional) This is used to determine base shift using preset values. The available profiles can be listed using --list_profile. The precedence is in the order of --base_shift < --auto < --profile.
  • --list_profile:
    (optional) Print the available profiles and exit.
  • --plot_limit INT (optional) the number of plots to be generated [default value: 1000].
  • --sig_plot_limit INT (optional) The maximum number of signal samples to draw on a plot [default value: 20000].
  • --bed FILE (optional) The bed file with annotations.
  • --no_colours (optional) hide base colours [default value: false].
  • --no_samples (optional) hide sample points [default value: false].
  • --save_svg (optional) save as svg. tweak --region and --xrange to capture the necessary part of the plot [default value: false].
  • --xrange (optional) initial x range [default value: 350].

plot_pileup

squigualiser plot_pileup [OPTIONS] -f genome.fasta -s reads.slow5 -a realign.sam -o output_dir --region chr1:20000-20400
squigualiser plot_pileup [OPTIONS] -f genome.fasta -s reads.slow5 -a realign.paf.gz -o output_dir --region chr1:20000-20400

Plot reference - signal alignment pileups.

  • -f, --file FILE:
    The sequence file in fasta/fa/fastq/fq/fq.gz format.
  • -s, --slow5 FILE Path to slow5 file containing raw signals.
  • -a, --alignment FILE Provide the .sam/.bam or .paf.gz file (generated using realgin or f5c eventalign).
  • --region STR [start-end] 1-based closed interval region to plot. For read-signal alignment eg:100-200. For reference-signal alignment eg: chr1:6811428-6811467 or chr1:6,811,428-6,811,467.
  • -o, --output_dir DIR :
    Specifies name/location of the output directory. A valid relative or absolute path can be provided. Data will be overwritten but the directory will not be recreated.
  • -r, --read_id STR (optional) Plot only the read with the read id specified.
  • -l, --read_list STR (optional) Path to a file containing a list of read_ids to plot only the reads listed.
  • --tag_name STR (optional) A tag name to easily identify the plot
  • -k, --kmer_length INT (optional) kmer length to consider for the base shift calculation and plotting.
  • --plot_reverse (optional) Plot only the reverse mapped reads.
  • --rna (optional) Specify if RNA reads are used. By default, only DNA is accepted.
  • --base_limit INT (optional) Maximum number of bases to plot.
  • --sig_scale (optional) Plot the scaled signal. By default, the signal is not scaled but converted to pA values. Supported scalings are: [medmad, znorm, scaledpA]. medmad is median absolute deviation scaling.
    znorm is zscore normalization scaling. scaledpA uses sc and sh tags to scale the raw signal to the pore model. The implementation of each method can be found at src/plot_utils.py/scale_signal()
  • --no_pa (optional) Do not convert the signal to pA levels. By default, the raw signal is converted to pA levels [default value: false].
  • --point_size INT (optional) Radius of the signal point drawn in the plot [default value: 0.5].
  • --base_width INT (optional) The base width when plotting with fixed base width [default value: 10].
  • --base_shift INT (optional) The number of bases to shift to align fist signal move [default value: 0]. More information on this can be found at here
  • --auto (optional) Calculate and automatically set the base shift. [default value: false]
  • --profile STR:
    (optional) This is used to determine base shift using preset values. The available profiles can be listed using --list_profile. The precedence is in the order of --base_shift < --auto < --profile.
  • --list_profile:
    (optional) Print the available profiles and exit.
  • --plot_limit INT (optional) the number of plots to be generated [default value: 1000].
  • --sig_plot_limit INT (optional) The maximum number of signal samples to draw on a plot [default value: 20000].
  • --bed FILE (optional) The bed file with annotations.
  • --plot_num_samples (optional) Annotate the number of samples for each move. By default, it is not annotated. Annotation can make the plots less responsive.
  • --overlap_bottom (optional) Plot the overlap at the bottom. By default, it is plotted at the top [default value: false].
  • --no_overlap (optional) Do not plot the overlap. By default, it is plotted at the top [default value: false].
  • --overlap_only (optional) Plot only the overlap [default value: false].
  • --cprofile (optional) Create a log file using python cprofile profiler [default value: false].
  • --return_plot (optional) Return the plot object without saving to output. This is used in plot_tracks tool [default value: false]. Cannot be used in conjunction with --output_dir.
  • --no_colours (optional) hide base colours [default value: false].
  • --save_svg (optional) save as svg. tweak --region and --xrange to capture the necessary part of the plot [default value: false].
  • --xrange (optional) initial x range [default value: 350].

plot_tracks

squigualiser plot_tracks [OPTIONS] -f commands.txt -s reads.slow5 -a reform.paf -o output_dir

Plot multiple reference - signal alignment pileup tracks.

  • -f, --file FILE:
    The file that contains the pileup_plot commands.
  • -o, --output_dir DIR :
    Specifies name/location of the output directory. A valid relative or absolute path can be provided. Data will be overwritten but the directory will not be recreated.
  • --tag_name STR (optional) A tag name to easily identify the plot
  • --shared_x (optional) Share x-axis so that all the plots move together [default value: false].
  • --auto_height (optional) Adjust track height automatically using the number of plots available in each track [default value: false].

calculate_offsets

squigualiser calculate_offsets [OPTIONS] -f reads.fasta -s reads.slow5 -a reform.paf -o output_dir

A utility program to calculate the most significant base index given a kmer model or a read - signal alignment.

  • -k, --kmer_length INT:
    (optional) kmer length to consider for the calculation.
  • --paf FILE:
    The read-signal alignment file generated using reform with -c option.
  • -f, --file FILE:
    The sequence file in fasta/fa/fastq/fq/fq.gz format.
  • -s, --slow5 FILE Path to slow5 file containing raw signals.
  • --model (optional) Path to the kmer model file if --use_model is true.
  • --use_model (optional) Calculate offset using the model file [default value: false]. By default, calculation is done for the reads using move table annotation.
  • --read_limit (optional) Limit the number of reads considered for the calculation [default value: 1000].
  • -r, --read_id STR (optional)Plot only the read with the read id specified.
  • -o, --output FILE :
    Specifies name/location of the output file. A valid relative or absolute path can be provided. Data will be overwritten. The extension should be .pdf. Output file can be used in --use_model mode or when a read id is specified (--read_id).
  • --tag_name STR (optional) A tag name to easily identify the plot
  • --rna:
    (optional) Specify if RNA reads are used. By default, only DNA is accepted [default value: false]. The tool will not error out if the data is RNA but if the user failed to specify it. It will still generate an incorrect output.

metric

squigualiser metric [OPTIONS] -f reads.fasta -s reads.slow5 -a reform.paf -o output.tsv
squigualiser metric [OPTIONS] -f reads.fastq -s reads.slow5 -a reform.paf -o output.tsv
squigualiser metric [OPTIONS] -f reads.fasta -s reads.slow5 -a realign.sam -o output.tsv
squigualiser metric [OPTIONS] -f reads.fasta -s reads.slow5 -a realign.paf.gz -o output.tsv

Parse the ss string to calculate basic statistics of the read/reference - signal alignments. The arguments are almost the same as for plot and plot_pileup tools. Instead of generating figures metric will generate statistics after parsing the ss string. These statistics are written to the output file.

  • -f, --file FILE:
    The sequence file in fasta/fa/fastq/fq/fq.gz format.
  • -r, --read_id STR (optional) Plot only the read with the read id specified.
  • -s, --slow5 FILE Path to slow5 file containing raw signals.
  • -a, --alignment FILE For read-signal alignment plots provide the path to .paf file generated using reform. For reference-signal alignment plots provide the .sam/.bam or .paf.gz file (generated using realgin or f5c eventalign).
  • --region STR [start-end] 1-based closed interval region to plot. For read-signal alignment eg:100-200. For reference-signal alignment eg: chr1:6811428-6811467 or chr1:6,811,428-6,811,467.
  • -o, --output FILE :
    Specifies name/location of the output file. A valid relative or absolute path can be provided. Data will be overwritten. These statistics are written to the output file.
  • --tag_name STR (optional) A tag name to easily identify the plot.
  • --plot_reverse (optional) Plot only the reverse mapped reads [default value: false].
  • --rna (optional) Specify if RNA reads are used. By default, only DNA is accepted [default value: false].
  • --sig_ref (optional) Plot signal to reference mapping. Can be mostly discarded. Act as a flag to avoid ploting reference-signal alignment using a .paf alignment file [default value: false].
  • --sig_scale (optional) Plot the scaled signal. By default, the signal is not scaled but converted to pA values. Supported scalings are: [medmad, znorm, scaledpA]. medmad is median absolute deviation scaling.
    znorm is zscore normalization scaling. scaledpA uses sc and sh tags to scale the raw signal to the pore model. The implementation of each method can be found at src/plot_utils.py/scale_signal()
  • --no_pa (optional) Do not convert the signal to pA levels. By default, the raw signal is converted to pA levels [default value: false].
  • --loose_bound (optional) Also plot alignments not completely within the specified region but at least part is [default value: false].
  • --base_shift INT (optional) The number of bases to shift to align fist signal move [default value: 0]. More information on this can be found at here
  • --profile STR:
    (optional) This is used to determine base shift using preset values. The available profiles can be listed using --list_profile
  • --list_profile:
    (optional) Print the available profiles and exit.
  • --plot_limit INT (optional) the number of plots to be generated [default value: 1000].
  • --sig_plot_limit INT (optional) The maximum number of signal samples to draw on a plot [default value: 20000].