Analysis

ncAnalyze

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###   Analysis of ncOrtho results   ###
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usage: ncAnalyze [-h] [-r <path>] [-o <path>] [-m <path>] [--skip [str]] [--include [str]] [--auto_skip [float]] [--iqtree [str]] [--mirnas [<path>]] [--ncrna_file [<path>]]

Analzye ncOrtho results. Gives: PhyloProfile input, supermatrix alignment, species tree.

Required Arguments:
  -r <path>, --results <path>
                        Path to ncOrtho output directory that is to be analyzed
  -o <path>, --output <path>
                        Path to location where output of analysis should be stored. Assumes that result files end with "_orthologs.fa"
  -m <path>, --mapping <path>
                        Tab seperated mapping file between NCBI taxonomy id and name of the query species or more generally the name of the directory that contains the ncOrtho results of each species(e.g "9606
                        Homo_sapiens")

Optional Arguments:
  --skip [str]          Comma separated list or path to newline seperated list of species for which analyses should be skipped
  --include [str]       Comma separated list or path to newline seperated list of species for which analyses should be performed. Will skip every species not in list.
  --auto_skip [float]   Exclude species for which less than a fraction of the reference miRNAs were detected from species tree calculation. (e.g. --auto_skip 0.5 means that only species in which at least 50%
                        of the reference miRNAs were found are used for species tree calculation) (Default: Off)
  --iqtree [str]        Call to iqtree. Do not change curly bracket notation (Default: iqtree -s {} -bb 1000 -alrt 1000 -nt AUTO -redo -pre {}/{})
  --mirnas [<path>]     Comma separated list or path to newline seperated file with miRNAs that should be used for reconstruction
  --ncrna_file [<path>]
                        Path to tab separated file of reference miRNAs information, as used in ncCreate and ncSearch. Uses mature sequence column to identify seed conservation.