diff --git a/_sources/change_log/index.rst.txt b/_sources/change_log/index.rst.txt index 3cb29487..e1ccd100 100644 --- a/_sources/change_log/index.rst.txt +++ b/_sources/change_log/index.rst.txt @@ -8,6 +8,10 @@ Change log Major changes to OrthoSNAP are summarized here. +**1.2.0** +Added the -rih (\-\-report_inparalog_handling) function, which creates +a summary file of which inparalogs where kept compared to trimmed + **0.1.0** Added -r/\-\-rooted, -st/\-\-snap_trees, and -ip/\-\-inparalog_to_keep functions diff --git a/_sources/usage/index.rst.txt b/_sources/usage/index.rst.txt index b5c00a4b..084576d8 100644 --- a/_sources/usage/index.rst.txt +++ b/_sources/usage/index.rst.txt @@ -81,29 +81,47 @@ or the inparalog with the median sequence length can be kept using the following Again, following transcriptomics, the default is to keep the longest sequence because (at least in theory) it is the most complete gene annotation. +Report inparalog handling +------------------------- +To report inparalogs and specify which was kept per SNAP-OG, use the -rih, \-\-report_inparalog_handling +argument. The resulting file, which will have the suffix ".inparalog_report.txt," will have three columns: |br| +- col 1 is the orthogroup file |br| +- col 2 is the inparalog that was kept |br| +- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon ";" |br| + +To generate this file, use the following command: + +.. code-block:: shell + + $ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -rih + +| + All options ----------- -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| Option | Usage and meaning | -+=============================+==============================================================================================================================================+ -| -h/\-\-help | Print help message | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| -v/\-\-version | Print software version | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| -t/\-\-tree | Input tree file (format: newick) | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| -s/\-\-support | Bipartition support threshold for collapsing uncertain branches (default: 80) | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| -o/\-\-occupancy | Occupancy threshold for identifying a subgroup of interest (default: 50%) | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| -r/\-\-roooted | boolean argument for whether the input phylogeny is already rooted (default: false) | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| -st/\-\-snap_trees | boolean argument for whether trees of SNAP-OGs should be outputted (default: false) | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| -ip/\-\-inparalog_to_keep | determine which sequence to keep in the case of species-specific inparalogs using sequence- or tree-based options (default: longest_seq_len) | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ -| -op/\-\-output_path | pathway for output files to be written (default: same as -f input) | -+-----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| Option | Usage and meaning | ++=====================================+==============================================================================================================================================+ +| -h/\-\-help | Print help message | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -v/\-\-version | Print software version | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -t/\-\-tree | Input tree file (format: newick) | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -s/\-\-support | Bipartition support threshold for collapsing uncertain branches (default: 80) | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -o/\-\-occupancy | Occupancy threshold for identifying a subgroup of interest (default: 50%) | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -r/\-\-roooted | boolean argument for whether the input phylogeny is already rooted (default: false) | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -st/\-\-snap_trees | boolean argument for whether trees of SNAP-OGs should be outputted (default: false) | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -ip/\-\-inparalog_to_keep | determine which sequence to keep in the case of species-specific inparalogs using sequence- or tree-based options (default: longest_seq_len) | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -op/\-\-output_path | pathway for output files to be written (default: same as -f input) | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ +| -rih, \-\-report_inparalog_handling | create a summary file of which inparalogs where kept compared to trimmed | ++-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+ *For genome-scale analyses, we recommend changing the -o/\-\-occupancy parameter to be the same for all large gene families so that the minimum SNAP-OG occupancy is the same -for all SNAP-OGs. \ No newline at end of file +for all SNAP-OGs. diff --git a/change_log/index.html b/change_log/index.html index a43dd142..0cf7aede 100644 --- a/change_log/index.html +++ b/change_log/index.html @@ -160,6 +160,9 @@

Change log

Major changes to OrthoSNAP are summarized here.

+

1.2.0 +Added the -rih (--report_inparalog_handling) function, which creates +a summary file of which inparalogs where kept compared to trimmed

0.1.0 Added -r/--rooted, -st/--snap_trees, and -ip/--inparalog_to_keep functions

1.0.0 diff --git a/index.html b/index.html index 270ebee4..87341bb2 100644 --- a/index.html +++ b/index.html @@ -238,6 +238,7 @@

Quick StartBasic usage
  • Accounting for tree uncertainty
  • Specifying which inparalog to keep
    • +
  • Report inparalog handling
  • All options
    • diff --git a/searchindex.js b/searchindex.js index 2275ef20..a889e472 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ 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log","FAQ","Quick Start","Other software","Tutorial","Usage"],titleterms:{The:0,about:0,account:6,all:6,basic:6,chang:1,clipkit:4,data:5,develop:0,download:5,faq:2,ggpubfig:4,handl:6,inparalog:6,inspect:5,keep:6,log:1,member:0,more:0,option:6,orthofish:4,orthosnap:5,other:4,output:5,phykit:4,quick:3,report:6,run:5,softwar:4,specifi:6,start:3,team:0,test:5,tree:6,treehous:4,tutori:5,uncertainti:6,usag:6,which:6}}) \ No newline at end of file diff --git a/usage/index.html b/usage/index.html index 78d1d4d0..c99a9c3b 100644 --- a/usage/index.html +++ b/usage/index.html @@ -92,6 +92,7 @@
  • Basic usage
  • Accounting for tree uncertainty
  • Specifying which inparalog to keep
    • +
  • Report inparalog handling
  • All options
    • @@ -234,12 +235,27 @@

    Specifying which inparalog to keep +

    Report inparalog handling

    +

    To report inparalogs and specify which was kept per SNAP-OG, use the -rih, --report_inparalog_handling +argument. The resulting file, which will have the suffix “.inparalog_report.txt,” will have three columns: |br| +- col 1 is the orthogroup file |br| +- col 2 is the inparalog that was kept |br| +- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon “;” |br|

    +

    To generate this file, use the following command:

    +
    $ orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -rih
+
    +
    +
    +

    +
    +

    All options

    --++ @@ -274,6 +290,9 @@

    All options

    + + +

    Option

    -op/--output_path

    pathway for output files to be written (default: same as -f input)

    -rih, --report_inparalog_handling

    create a summary file of which inparalogs where kept compared to trimmed

    *For genome-scale analyses, we recommend changing the -o/--occupancy parameter to be the same for all large gene families so that the minimum SNAP-OG occupancy is the same