Jerome Kelleher jeromekelleher
jeromekelleher
/ divergence_matrix.py
Created
October 24, 2022 11:25
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| # Efficient computation of the pairwise divergence matrix. | |
| import time | |
| import itertools | |
| import msprime | |
| import tskit | |
| import numba | |
| import numpy as np | |
jeromekelleher
/ branch_grm_incremental.py
Created
October 14, 2022 16:31
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| import sys | |
| import tskit | |
| import numpy as np | |
| import numba | |
| @numba.njit | |
| def _normalise(B): | |
| K = np.zeros_like(B) | |
| N = K.shape[0] |
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| import sys | |
| import tskit | |
| import numpy as np | |
| import numba | |
| @numba.njit | |
| def sv_tables_init(parent_array): | |
| # This is an implementation of Schieber and Vishkin's nearest common ancestor | |
| # algorithm from TAOCP volume 4A, pg.164-167 [K11]_. Preprocesses the |
jeromekelleher
/ better_animate_edges.py
Created
April 14, 2019 14:21
Animate trees evolving along a chromosome
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| import pathlib | |
| import subprocess | |
| import tempfile | |
| import tskit | |
| import msprime | |
| def draw_transitioning_tree(tree, filename, edge_colours): | |
| tree.draw( |
jeromekelleher
/ animate_edges.py
Created
April 13, 2019 17:18
Animate trees evolving along a tree sequence
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| import pathlib | |
| import subprocess | |
| import msprime | |
| def draw_partial_tree(tables, edges, filename): | |
| tables.edges.clear() | |
| for edge in edges: | |
| tables.edges.add_row(*edge) |
jeromekelleher
/ gist:074ac7f7e0f0c95a7be4
Created
August 13, 2015 11:44
Stacktrace of htslib error.
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| (gdb) run scripts/download_data.py | |
| Starting program: /usr/bin/python scripts/download_data.py | |
| [Thread debugging using libthread_db enabled] | |
| Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". | |
| Cleaning out directory '/home/jk/work/github/server/ga4gh-downloaded-data/dataset1/reads/low-coverage' | |
| Downloading index for 'ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam' | |
| [M::test_and_fetch] downloading file 'ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai' to local directory | |
| Writing 'HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam' | |
| *** buffer overflow detected ***: /usr/bin/python terminated | |
| ======= Backtrace: ========= |