1. 24 Apr, 2021 2 commits
  2. 23 Apr, 2021 4 commits
    • Cecilia-Sensalari's avatar
      Rename parameters in configuration file (#17) · 4adfa887
      Cecilia-Sensalari authored
      * Rename parameter "max_number_outgroups"
      * Rename parameter (consensus multiple outgroups)
      * Rename parameter (y_axis_max_limit_paralogs_plot)
      * Rename parameter (max_ks_paralogs)
      * Rename parameter (max_ks_orthologs)
      * Rename parameter (collinearity)
      * Rename parameter (bin_width_paralogs)
      * Rename parameter (bin_width_orthologs)
    • Cecilia-Sensalari's avatar
      Rename and describe headers in output files (#14) · 487813ba
      Cecilia-Sensalari authored
      * Rename headers of both adjustment table files
      * Rename header "Focal_Species" in trios file
      * Rename ortholog DB header, remove DB median data
      * Add adjust. table description in input_output.rst
      * Add subsections in output file list (docs)
    • Cecilia-Sensalari's avatar
      Docs: interactive containers and WSL2 notes (#16) · 181c2dc9
      Cecilia-Sensalari authored
      * Add interactive container for manual pipeline
      * Mounting Windows filesystem in WSL2
      - Explain how to access the Windows
      file system from the WSL2 terminal,
      which by default is initialized in the
      Linux home.
      - Singularity commands in WSL2 need to
      manually mount the Windows file system
      within the container.
    • Cecilia-Sensalari's avatar
      Reorder local installation steps in documentation (#15) · c8012e2d
      Cecilia-Sensalari authored
      - First install non-Python dependencies and
      lastly the package itself (with pip3)
      - Add "sudo apt-get update" in step 1
      - Add install python3-pip (for pip3) in step 1
      - Remove redundant link to paml docs
      - Fuse the cloning and pip3 steps in one step
      * WSL2: manual mounting of Windows filesystem
      - Add note about how to mount the Windows
      file system in the WSL2 terminal, which is
      initialized by default in the Linux home.
  3. 14 Apr, 2021 2 commits
  4. 13 Apr, 2021 2 commits
  5. 08 Apr, 2021 1 commit
    • Cecilia-Sensalari's avatar
      Generate ortholog PDFs when data are unavailable (#10) · 0113723a
      Cecilia-Sensalari authored
      - If there are missing species pairs in the DBs,
      generate a PDF figure only if at least one trio has
      complete data (Ks list and Ks peak estimate).
      - Log warnings when skipping a trio due to
      missing data in DBs.
      - The missing pairs are listed at the end, as
      missing 1) from both databases, 2) from only 
      peak DB and 3) from only Ks list DB.
      - Note: if the ortholog peak DB isn't present but
      the Ks list DB is complete, the distributions
      will still be plotted, all without their modes.
  6. 06 Apr, 2021 1 commit
    • Cecilia-Sensalari's avatar
      PAML installation from source (#7) · 3798044c
      Cecilia-Sensalari authored
      * Change PAML installation (from source)
      * Paml instructions in installation.rst
      * Improve container docs (installation.rst)
      * Update comments in Dockerfile and Singularity file
      * Remove squared brakets in NF command
      * Rename Paralog --> Ortholog in ortholog TSV file
      * Remove redundant color argument in modeling.py
      * Update to tool name "ksrates" in the license
      * Rename "wgd" module to "wgd_ksrates"
      * Replace "wgd" with "wgd_ksrates" in container file
      * Update license (author and year)
      * Update installation.rst (link to singularity docs)
      * Add note in local installation about Windows users
      * Remove installation commands through bioconda
  7. 30 Mar, 2021 3 commits
  8. 29 Mar, 2021 1 commit
  9. 25 Mar, 2021 3 commits
    • Cecilia-Sensalari's avatar
      Update Documentation (concept and input_output) (#2) · a6e40622
      Cecilia-Sensalari authored
      * Update concept.rst
      * Update input_output.rst
      * Update usage.rst (file paths and descriptions)
      * Delete .buildinfo
      * Describe ks.tsv file format
      * Add (E)LMM file format description; internal links
      * Add (E)LMM file figures
      * Rename header in ELMM TSV file
      * Restructure mixture model section and add table
      * Reduce paralog analyses description in docs
      * Add Note block in input_output.rst about filenames
      * Rename header in main.nf
      * Add preprint DOI in "How to cite us" doc page
      * Replace <focal species> with species (filename)
    • Cecilia-Sensalari's avatar
      Ks plots without divergence lines have inner legend (#4) · 907afe37
      Cecilia-Sensalari authored
      * Ks plot without divergence lines has inner legend
      * Anchor cluster plot without lines has inner legend
      * Exp-log plot without lines has inner legend
      * Lognormal plot without lines has inner legend
      * Reduce right margin of simple plots
      * Ask matplotlib>=3.3.3 to fix a compatibility issue
    • Cecilia-Sensalari's avatar
      Anchor weights (#5) · ba1fd0fa
      Cecilia-Sensalari authored
      * Anchor weights (also in paralogs-analyses command)
      * Set the number of components to 3 in test dataset
      * Rename function in anchor weighting
      * Move compute_weight; del 0.05 in ks_list_from_tsv
  10. 18 Mar, 2021 1 commit
    • Cecilia-Sensalari's avatar
      Merge dev into master (#1) · a401f78b
      Cecilia-Sensalari authored
      * Rename with 'focal species'
      Rename 'species of interest' and 'main species' in documentation RST files,
      function docstrings, comments in code, in config_elaeis.txt, but also
      in some actual code lines: in generate_config.py and fc_configfile.py
      ('focal_species' field), in main.nf (parse config file in setup process).
      * renaming gff_filename field
      * Rename (adjustment arrows, bootstrap iterations)
      * Improve parameter description in configuration.rst
      * Rename "adjustment" in filenames and python output
      * Rename rates: branch contribution or ks distances
      * Rename "adjustment" (leftover)
      * Describe logging level in configuration.rst
      * Add database names in input_output.rst
      * Rename peak_stats
      * Rename focal species in readme
      * Catch missing species in fasta_filenames
      * Catch missing species in latin_names and exit
      * Bugfix for catch missing species in latin_names
      * Bugifx to catch missing species in latin_names
      * Rename max_mixture_model_ks
      * Add parameter default values in configuration.rst
      * Correct RST syntax
      * Add output directory and filenames to docs
      * Remove AIC and BIC PDFs
      * Catching missing species WIP
      * Remove unnecessary newick_tree variable
      * Improve checking steps for FASTA and latin names.
      Exit if latin_names is empty or one or more species are missing.
      The new function check_complete_dictionary() lists the missing
      species in latin_names and exits.
      Check and warn if FASTA of GFF files are missing; exit after all
      the files have been checked.
      * Update test_pipeline.yml
      * Update README.md
      * Update doc/source/concept.rst
      * Update doc/source/configuration.rst
      * Update ksrates/fc_configfile.py
      * Update doc/source/configuration.rst
      * Update doc/source/paralogs_analyses.rst
      * Update ksrates/correct.py
      * Update ksrates/fc_rrt_correction.py
      * Accept suggestions by reviewer about renaming
      * Rename function "decompose_ortholog_ks"
      * Rename function to check file content
      * Rename function to check complete latin_names
      * Removing comment about Nextflow in plot_tree.py
      * Rename back to "species of interest" in wgd files
      * Mention GFF file in "colinearity" config field
      * Move logging message in setup_correction.py
      * Rename "colinearity" to "anchors" in LMM filenames
      * Change figure title of anchor Ks clustering picture
      * Rename to "focal species" in readme
      * Fix RST title
      * Link to "paralogs analyses" from expert config
      * Apply suggestions from code review
      * Replace GFF dict with string; improve checkpoints
      * Remove unnecessary function argument
      Co-authored-by: Cecilia SENSALARI's avatarcesen <cesen@psb.ugent.be>
      Co-authored-by: default avatarlohausr <56632794+lohausr@users.noreply.github.com>
  11. 12 Mar, 2021 2 commits
  12. 09 Mar, 2021 2 commits
  13. 04 Mar, 2021 1 commit
  14. 02 Mar, 2021 2 commits
  15. 01 Mar, 2021 3 commits
  16. 28 Feb, 2021 10 commits