gpseq_fromfish_merge

To merge the output of multiple datasets into a set of single merged tables (usually convenient to explore the data and generate plots), we designed the gpseq_fromfish_merge tool.

Run gpseq_fromfish_merge with no parameters for a brief recap of all the options. Run it with -h for a detailed help page.

usage: gpseq_fromfish_merge [-h] -m metadata -i indir [indir ...] [-o outdir]
                            [-a Z Y X] [-d sep] [-t nthreads] [--version]

Merge gpseq_fromfish outputs, add dataset and cell type information. The script
looks for the output in subfolders of the specified input directories. These
subfolders must be named as dataset_series, with series being in XXX format with
leading zeros (e.g., iJC001_001, iJC001_002, iJC002_001). Please, note that the
channel is enforced as lower-case by the merge operation.

The script will not only merge the input, but also produce a table of
informative homologue copy pairs features, if any pair is found in the input.

Example 1: output in current directory.
gpseq_fromfish_merge -m meta.tsv -i HAP1/dots_auto IMR90/dots_auto

Example 2: output to "/home/user/out" directory.
gpseq_fromfish_merge -m meta.tsv -i HAP1/dots_auto IMR90/dots_auto
        -o /home/user/out

optional arguments:
  -h, --help            show this help message and exit
  -m metadata, --meta metadata
                        Path to metadata table. Required columns: dataset,
                        series, channel, cell_line, probe_label.
  -i indir [indir ...], --indir indir [indir ...]
                        List of space-separated input folder paths with
                        gpseq_fromfish output as subfolders.
  -o outdir, --outdir outdir
                        Path to output folder, created if missing. Defaults to
                        current position.
  -a Z Y X, --aspect Z Y X
                        Physical size of Z, Y and X voxel sides. Default:
                        300.0 130.0 130.0
  -d sep, --delimiter sep
                        Column separator in input tables.
  -t nthreads, --threads nthreads
                        Number of threads to be used for parallelization.
                        Increasing the number of threads might increase the
                        required amount of RAM.
  --version             show program's version number and exit