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Ben J Woodcroft wwood

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wwood / gist:34e2ae1d2daf1e88badb7877e0a42bea
Created June 14, 2025 23:01
✗ pixi run -e dev ../admin/check_versions.py
🔍 Checking dependency versions...
🔍 Discovering environments...
Found environments: default, dev, metabuli, singlem, chopper, fastqc, nanoplot, quast, bbmap, flye, polishing, pilon, minimap2, spades, pysam, mfqe, final-assembly, seqkit, metabat2, checkm, checkm2, coverm, das-tool, rosella, maxbin2, concoct, vamb, taxvamb, taxvamb-gpu, semibin, semibin-gpu, comebin, comebin-gpu, eggnog, gtdbtk, pggb
Checking all environments: default, dev, metabuli, singlem, chopper, fastqc, nanoplot, quast, bbmap, flye, polishing, pilon, minimap2, spades, pysam, mfqe, final-assembly, seqkit, metabat2, checkm, checkm2, coverm, das-tool, rosella, maxbin2, concoct, vamb, taxvamb, taxvamb-gpu, semibin, semibin-gpu, comebin, comebin-gpu, eggnog, gtdbtk, pggb
📦 Checking environment: default
==================================================
@wwood
wwood / public_metagenome_size.sql
Created February 20, 2023 01:04
Estimate the total amount of public metagenome sequence using Google BigQuery
-- Loop counter
DECLARE counter int64 default 1;
-- Create intermediate table with organisms that are metagenomes
CREATE OR REPLACE TABLE test.emp
AS
WITH cte AS
(
SELECT 1 AS xlevel, tax_id, parent_id, sci_name
@wwood
wwood / example.smk
Created November 2, 2022 02:48
samples = [1,2,3,4,5]
rule all:
input:
"test.out"
rule a:
output:
@wwood
wwood / gist:e4cb06b19e01af74fe05d31e8199a9e0
Created October 19, 2021 02:49
options(repr.plot.width=15)
analyse <- function(current_samples, p0) {
# p0 = 0.5
print("Current samples:")
print(current_samples)
proportion = sum(current_samples<(p0*n))
print(paste("Proportion less than",p0*n,'is',proportion,"out of",length(current_samples)))
binom_test_result = binom.test(proportion, length(current_samples), p=p0)
@wwood
wwood / sequence1.fna
Last active April 30, 2020 09:09
fastani issue seqs
>sequence1
CATCCTTTAACAATAGCCGTAGCCTTCACTTTTTTCTGGCTGCTTGGCCTGTTGTCGGTATTTGGTTTGCTGCTCTGGGTGTGTCTACAATGGCTTTTAATCTTAACGGTTTCAATTTTAACCAGTCCCTACTGGATAGTCAGGGGCGTGTTGTGCGTACTTGGGCTGACATCCTTAACCAAGCTAACCTTGGATTTGAAGTCATGCACGAACGTAATGCGCACAACTTTCCGCTAGACCTCGCTGCAGCAGACGTAACTCCTGTTGCTCTTACTGCACCTGCTGTAGGCTAATCTCCGTCCGTTCATCCCTCACAAGGGACGCATGAAGTTTGATCATGGAACGGGGGTCAAACACTTGGAGATTATCATGGCTTATCAAGTCACCTACAAGTATCGCGGCGTTTCTTACACTAAAACGGTAGTCCGTTAAAGCGGCATTGGGAGGTGCAAACCCTCCCTTACCTATTGGCGTTGGCCCTTACGAGGACACCCTTCGCCGTCTAGACGGTGGGATAGACCACAATAAAAACCCGAAAAAAATTTTCCAAAGCTTTGGAGAGAACCTATTTGTAATTTCTCTCTTTTTTAAAAATGGCACAACAAGCTGGCTCTGGTCTGCTTCAGTCTGCACTGACGCGTCCAGGCTCTCTTAATGGTGCGGCAGATGCCCGCGCCCTGTATCTCAAGCTTTTTAGCGGTGAGATGTTCAAAGGCTTCCAGCACAATGCGATCGCTCGTGACCTTGTGATGAAGCGCACCCTCAAGGGTGGCAAGAGTCTCCAGTTCATCTACACTGGACACACTCAAGCTGAGTTCCATACCCCCGGTCGGGCTATTCTTGGTAATGACCAGGGTGCTCCCCCGGTGGCTGAGAAGACCATCACCTGTGATGACCTTCTGATCAGCTCGGCTTTCCTGTACGAACTCGATGAAGTTCTGTCTCATTACGATCTGCGTAGTGAGATCTCCCGTAAGATCGGCTATGCTCTGGCTCAGAAGTATGACCGTCTG
@wwood
wwood / plasmid_and_random.fna
Created April 27, 2020 05:28
plasmid_and_random.fna for plasmidVerify
>random_sequence_length_50000_1
CCGTCACGATCATAAGCCCAGGTATTTTCTCATAGGATTAAGCCTTAGCTCCGTACAAGCCAAGCGCTAACGAACGTAGCTCGGGAATTAGCCGTACATAATGACTGCCGGCATGACATAAAGTGGCAGATTTGCAAAATTTGCTCGTACCTCCGGATTTGCTCCTGATCTCCGTTACAATGTGGTCTCTATAGACTGGTAAATCCCATTTAGGCCGAATTGTAGCGGACCAATGCCCCTAGATGAACTCAATGACCACCCACGTTGCCGACATAAATAGGCATCCTGGGTCTCTGGAGGAGCATAGCCGGGATTAGCATGTATTGGAACAGATACGACGATTGGAATAAGTCGGCAGGACGTCACGATGCCCACCTTTCGTGGTATTCTTCGATATTAGCTGACTCCTTGGGTTCTGAGGACATCGAATTTTTATGTGTTTAGACTAACCCACTAATTATTGACGAAGGACTCGATTAACTGGCATTTTGCGCACCGTCTCTTATTTGACGGCAAGTAGCAGTCTAGCACACGACCTAGTGAGCAAAAATACTTCCTTGTGAGACGGGCGGTCTAGCGGCGTGGCTAAGGTAAAAGAAACGGCGCAAGCGCTACCCTAGCGCGGCGTAGCCGATCACACACCGGTCCCGCAGGAGCCAGCGCATTGCGGGTTGGTACAACCAAAGAGGAATCGGTGTCGCGGAACGATAACTTTGAATTAGGTCAGGTTCTTTAAAGACTGTTCTCACCTGAAATTCATTTAGACTGTTCCCGGGCGCCATTGAGATCGTAATCCGGCCCACGGTGATACAAGTCCTTTACGATACATATGCGGGTGCAAGCCACCCAACTGCCCATCGCCCTTTCATCTGCCCCAGAAGCGGGGACCCGAAATTGAAGGACACTAATAAATTGACGTAATGTACGGTAATAAAGAATCTGGTAGGGTGCCCCACTCCATGTTGAGAGGATTGCCTCATCGCCCTAAACGT
@wwood
wwood / ecoli100.1.head1000.fq
Last active October 21, 2019 22:42
ecoli100.1.head1000.fq.gz
@NS500333:300:HNGK5AFXY:1:11101:14311:1054 1:N:0:GGAGCTAC+NTTAGACG
CGGGTNCACTGCATCTTCACAGCGAGTTCAATTTCACTGAGTCTCGGGTGGAGACAGCCTGGCCATCATTACGCCA
+
AAAAA#EEEEEEEEEEEEA6EEEEEEEE<EEEEEE/EEEEEEEEEEEEEEEEEEE/EEEE/EEEEEEEAEEE<AE<
@NS500333:300:HNGK5AFXY:1:11101:22036:1054 1:N:0:GGAGCTAC+NTTAGACG
GTTCCNGGCCGGACCGCTGGCAACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACA
+
AAAAA#EEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEEE/EEEEAEEEEAEEEEE/AEEEAEEEEEEEEEE<E/
@NS500333:300:HNGK5AFXY:1:11101:13098:1055 1:N:0:GGAGCTAC+NTTAGACG
TTAGCNAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGG
@wwood
wwood / _dbg.txt
Created January 14, 2018 05:26
_dbg.txt
~/git/mrustc/output$ tail *_dbg.txt
==> liballoc.hir_dbg.txt <==
(0.00 s) MIR Validate PO: DONE
MIR Validate Full: V V V
(0.00 s) MIR Validate Full: DONE
Trans Enumerate: V V V
(0.00 s) Trans Enumerate: DONE
Trans Codegen: V V V
Running comamnd - "gcc" "-ffunction-sections" "-pthread" "-O2" "-g" "-o" "output/liballoc.hir.o" "output/liballoc.hir.o.c" "-c"
(0.01 s) Trans Codegen: DONE
@wwood
wwood / ngs-bits build
Last active September 13, 2017 07:05
phase `unpack' succeeded after 0.5 seconds
starting phase `patch-usr-bin-file'
phase `patch-usr-bin-file' succeeded after 0.0 seconds
starting phase `patch-source-shebangs'
phase `patch-source-shebangs' succeeded after 0.2 seconds
starting phase `patch-generated-file-shebangs'
phase `patch-generated-file-shebangs' succeeded after 0.0 seconds
starting phase `build'
cd bamtools && rm -rf bin build lib include src/toolkit/bamtools_version.h
mkdir bamtools/build
@wwood
wwood / roary-build.log
Last active July 22, 2016 11:53
starting phase `check'
t/00_requires_external.t
1..8
ok 1 - blastp in PATH
ok 2 - makeblastdb in PATH
ok 3 - mcl in PATH
ok 4 - mcxdeblast in PATH
ok 5 - bedtools in PATH
ok 6 - prank in PATH
ok 7 - parallel in PATH