JCVI

报错：AttributeError: 'LayoutLine' object has no attribute 'color'
解决办法：removed bottom blank line in "layout" file删掉layout最后一行的空格

$ python -m jcvi.compara.catalog ortholog
Usage:
    catalog.py ortholog species_a species_b

    Run a sensitive pipeline to find orthologs between two species a and b.
    The pipeline runs LAST and generate .lifted.anchors.

    `--full` mode would assume 1-to-1 quota synteny blocks as the backbone of
    such predictions. Extra orthologs will be recruited from reciprocal best
    match (RBH).


Options:
  -h, --help            Show this help message and exit
  --dbtype=DBTYPE       Molecule type of subject database, must be one of
                        nucl|prot [default: nucl]
  --full                Run in full 1x1 mode, including blocks and RBH
                        [default: False]
  --cscore=CSCORE       C-score cutoff [default: 0.7]
  --dist=DIST           Extent of flanking regions to search [default: 20]
  -n N, --min_size=N    Minimum number of anchors in a cluster [default: 4]
  --quota=QUOTA         Quota align parameter [default: none]
  --exclude=EXCLUDE     Remove anchors from a previous run [default: none]
  --no_strip_names      Do not strip alternative splicing (e.g. At5g06540.1 ->
                        At5g06540) [default: False]
  --liftover_dist=LIFTOVER_DIST
                        Distance to extend from liftover. Defaults to half of
                        --dist [default: none]
  --cpus=CPUS           Number of CPUs to use, 0=unlimited [default: 8]

  Dot plot parameters:
    --skipempty         Skip seqids that do not have matches [default: False]
    --nochpf            Do not change the contig name [default: False]
    --nostdpf           Do not standardize contig names [default: False]
    --genomenames=GENOMENAMES
                        Genome names for labeling axes in the form of
                        qname_sname, eg. "*Vitis vinifera*_*Oryza sativa*"
                        [default: disabled]
    --theme=THEME       Color index within the palette for contig grid
                        boundaries. Palette contains: #E41A1C|#377EB8|#4DAF4A|
                        #984EA3|#FF7F00|#FFFF33|#A65628|#F781BF|#999999, must
                        be one of 0|1|2|3|4|5|6|7|8 [default: 2]

JCVI utility libraries v1.0.13 [Copyright (c) 2010-2020, Haibao Tang]

$ python -m jcvi.compara.synteny scree
[error] scree not a valid ACTION

Did you mean one of these?
    screen

Usage:
    python -m jcvi.compara.synteny ACTION


Available ACTIONs:
      assemble | Build blocks from regions defined by start and end
    breakpoint | Identify breakpoints where collinearity ends
          coge | Convert CoGe file to anchors file
         depth | Calculate the depths in the two genomes in comparison
    fromaligns | Convert aligns file to anchors file
        layout | Compute layout based on .simple file
      liftover | Given anchor list, pull adjacent pairs from blast file
        matrix | Make oxford grid based on anchors file
        mcscan | Stack synteny blocks on a reference bed
       mcscanq | Query multiple synteny blocks
         query | Collect matching region based on the query region
       rebuild | Rebuild anchors file from prebuilt blocks file
          scan | Get anchor list using single-linkage algorithm
        screen | Extract subset of blocks from anchorfile
        simple | Convert anchorfile to simple block descriptions
           spa | Convert chr ordering from SPA to simple lists
         stats | Provide statistics for mscan blocks
       summary | Provide statistics for pairwise blocks
      toaligns | Convert anchors file to aligns file

JCVI utility libraries v1.0.13 [Copyright (c) 2010-2020, Haibao Tang]