campanam / ucealnstats

Calculate taxon-specific alignment statistics from a collection of UCE alignments

ucealnstats

Michael G. Campana, 2020
Smithsonian Institution

Script to calculate taxon-specific alignment statistics from a collection of ultraconserved element (UCE) alignments

Creative Commons 0 Waiver

To the extent possible under law, the Smithsonian Institution has waived all copyright and related or neighboring rights to ucealnstats; this work is published from the United States. You should have received a copy of the CC0 legal code along with this work. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Citation

We politely request that you cite this script as:
Campana, M.G. 2020. ucealnstats. Smithsonian Institution. https://github.com/campanam/ucealnstats.

Installation

Clone the repository: git clone https://github.com/campanam/ucealnstats
Make the ucealnstats.rb script executable: chmod +x ucealnstats/ucealnstats.rb
Move the ucealnstats.rb script to a target destination: mv ucealnstats/ucealnstats.rb <destination>

Usage

Input

The ucealnstats.rb script expects the UCE alignments to be contained within a single directory. UCE alignments should be in NEXUS format with '.nex' or '.nexus' extensions.

Execution

Execute the script using the command ruby ucealnstats.rb <directory of UCE alignments>. Output can be redirected from standard output to a file using >, e.g. the command ruby ucealnstats.rb test_dir > test_results.tsv will collect alignment statistics from UCE alignments within the directory 'test_dir' and print them to the file 'test_results.tsv'.

Output

The script will output results in tab-separated values (TSV) format.

The script will print the following overall statistics:

1. Results for : Name of target directory analyzed by the script.
2. Total No. of Loci: Total number of UCE alignments with the target directory.
3. Total UCE Alignment Length: Total concatenated length (in bp) of UCE alignments.

The script will then print per-sample alignment statistics:

1. Sample: Name of the sample.
2. CapturedUCEs: Number of UCE alignments that included the sample.
3. MissingUCEs: Number of UCE alignments that excluded the sample (i.e. 100% missing data for a sample at that locus).
4. GappedAlignmentLength: Total concatenated UCE alignment length for the sample including gaps due to indels, but excluding missing data.
5. UngappedAlignmentLength: Total concatenated UCE alignment length for the sample excluding both gaps due to indels and missing data.
6. TotalLengthCapturedUCEs: Total length of UCE alignments for which some data for the sample was generated (including gaps and missing data).
7. MeanGapped(Missing): Sample mean gapped UCE lengths including missing loci.
8. MeanUngapped(Missing): Sample mean ungapped UCE lengths including missing loci.
9. MeanGapped(NoMissing): Sample mean gapped UCE lengths excluding missing loci.
10. MeanUngapped(NoMissing): Sample mean ungapped UCE lengths excluding missing loci.
11. Coverage(Missing): Sample coverage including missing loci defined as GappedAlignmentLength/Total UCE alignment length.
12. Coverage(NoMissing): Sample coverage excluding missing loci defined as GappedAlignmentLength/TotalLengthCapturedUCEs.