Command line interface

While IsoTools is designed to be run interactivly (e.g. in a python notebook, or in the repl), it can also be run as a command line tool, with predefined parameters. This may be convenient to process different experiments in a standardized pipeline. For example usage, see the CLI tutorial.

process LRTS data with isotool

usage: run_isotools [-h]
                    [--anno <file.gtf/gff/gff3[.gz]>]
                    [--genome <file.fasta>]
                    [--samples <samples.tsv>]
                    [--file_prefix </output/directory/prefix>]
                    [--file_suffix <suffix>]
                    [--short_read_samples <samples.csv>]
                    [--force_recreate]
                    [--no_pickle]
                    [--progress_bar]
                    [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL,None}]
                    [--group_by <column name>]
                    [--custom_filter_tag [<TAG="expression"> ...]]
                    [--filter_query <"expression">]
                    [--qc_plots]
                    [--altsplice_stats]
                    [--transcript_table]
                    [--gtf_out]
                    [--diff [<group1/group2> ...]]
                    [--diff_plots <n>]
                    [--plot_type <type>]
                    [--plot_dpi <dpi>]
                    [--altsplice_plots <n>]

Named Arguments

--anno

specify reference annotation

--genome

specify reference genome file

--samples

add samples from sample tsv

--file_prefix

Specify output path and prefix.

Default: “./”

--file_suffix

Specify output sufix (not used for pickle).

--short_read_samples

Specify tsv with short read samples.

--force_recreate

reimport transcriptomes from alignments, even in presence of pickle file.

Default: False

--no_pickle

Do not pickle the transcriptome for later use.

Default: False

--progress_bar

Show the progress of individual tasks.

Default: False

-l, --log

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, None

Set the logging level.

Default: “INFO”

--group_by

specify column used for grouping the samples. This applies to –qc_plots, –altsplice_stats, –diff, –diff_plots and –altsplice_plots

Default: “name”

--custom_filter_tag

add custom filter tag

--filter_query

filter the transcripts used in gtf and table output

Default: “FSM or not (INTERNAL_PRIMING or RTTS)”

--qc_plots

make qc plots

Default: False

--altsplice_stats

alternative splicing barplots

Default: False

--transcript_table

make transcript_table

Default: False

--gtf_out

make filtered gtf

Default: False

--diff

perform differential splicing analysis

--diff_plots

make sashimi plots for <n> top differential genes

--plot_type

Possible choices: png, pdf, svg, eps, pgf, ps

Default: “png”

--plot_dpi

Specify resolution of plots

Default: 100

--altsplice_plots

make sashimi plots for <n> top covered alternative spliced genes for each category