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post_validation

README.md

This directory contains a series of tools that can be used to post-validate the simulation output produced by FAVITES.

  • compare_contact_networks.py: Compare a given simulated contact network against a reference contact network

    • Compare distribution of node degrees
    • Usage: compare_contact_networks.py [-h] -r REF -s SIM
      • REF: Reference contact network (FAVITES format)
      • SIM: Simulated contact network (FAVITES format)

  • compare_trees.py: Compare a given simulated tree against a given reference tree

    • Compare distributions of all branch lengths, internal branch lengths, terminal branch lengths, and root-to-tip distances
    • Usage: compare_trees.py [-h] -r REF -s SIM [-n NW_DISTANCE]
      • REF: Reference tree (Newick format)
      • SIM: Simulated tree (Newick format)
      • NW_DISTANCE: Path to nw_distance executable (if not in PATH)

  • distribution_distance.py: Compute a distance between the distributions of two given samples

    • Input distribution samples should contain a single sample per line
    • Usage: distribution_distance.py [-h] -1 DIST1 -2 DIST2 [-d DISTANCE] [-n NUM_POINTS]
      • DIST1: File containing samples from distribution 1
      • DIST2: File containing samples from distribution 2
      • DISTANCE: The distance to compute
        • jsd: Jensen-Shannon Divergence
        • jsm: Jensen-Shannon Metric
        • ks: Kolmogorov-Smirnov Distance (returns a (distanc, p-value) tuple)
      • NUM_POINTS: Number of Points when Discretizing PDF (used in jsd, jsm)

  • ltt.py: Create an LTT plot from one or more Newick trees

    • Usage: ltt.py [-h] [-p PRESENT_DAY [PRESENT_DAY ...]] [-t TITLE] [-xl XLABEL] [-yl YLABEL] [-xmin XMIN] [-xmax XMAX] [-ymin YMIN] [-ymax YMAX] tree [tree ...]
      • PRESENT_DAY: Present day times (time of furthest distance from root) for each of the input trees
      • TITLE: Figure title
      • XLABEL: X-axis label
      • YLABEL: Y-axis label
      • XMIN: Minimum X value
      • XMAX: Maximum X value
      • YMIN: Minimum Y value
      • YMAX: Maximum Y value
      • tree: Tree(s) (Newick format)

  • sequence_score_profile_HMM.py: Score a given sequence dataset against a given profile HMM

    • Usage: sequence_score_profile_HMM.py [-h] -H HMM -s SEQ [-q] [-a HMMSEARCH]
      • HMM: Profile HMM (HMMER format)
      • SEQ: Sequence file
      • -q: Input file is FASTQ (not FASTA)
      • HMMSEARCH: Path to hmmsearch executable (if not in PATH)