Skip to content

Instantly share code, notes, and snippets.

View pmcarlton's full-sized avatar

Peter Carlton pmcarlton

6 followers · 7 following
View GitHub Profile
@pmcarlton
pmcarlton / amino acids
Created October 3, 2023 06:56
Here are the 20 naturally-occurring amino acids and some of their properties.
Code Short Mnemonic Charge MolWt Properties
A Ala alanine 0.0 71.0788 tiny,small,aliphatic,nonpolar
C Cys cysteine 0.0 103.1388 tiny,small,nonpolar
D Asp aspartate -1.0 115.0886 small,polar
E Glu glutamate -1.0 129.1155 polar
F Phe phenylalanine 0.0 147.1766 aromatic,nonpolar
G Gly glycine 0.0 57.0519 tiny,small,nonpolar
H His histidine +0.5 137.1411 aromatic,polar
I Ile isoleucine 0.0 113.1594 aliphatic,nonpolar
K Lys lysine +1.0 128.1741 polar
@pmcarlton
pmcarlton / 20230106-canu-DRR424710.log
Created February 2, 2023 00:20
Log of canu assembly of DRR424710.all_reads.fq into drr0-n2-g0.contigs.fasta
>> time ~/code/canu-2.2/bin/canu -d ~/canurun1/ -p drr0-n2-g0 hapMemory=4 hapThreads=4 maxMemory=12 maxThreads=8 genomeSize=100m batMemory=8 batThreads=2 -nanopore DRR424710.all_reads.fq
-- canu 2.2
--
-- CITATIONS
--
-- For 'standard' assemblies of PacBio or Nanopore reads:
-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
-- Genome Res. 2017 May;27(5):722-736.
-- http://doi.org/10.1101/gr.215087.116
@pmcarlton
pmcarlton / 20230201longstitch-log.txt
Created February 2, 2023 00:12
2023-02-01 LongStitch issue#62 log
>> longstitch -d run draft=drr0-n2-g0.contigs reads=DRR424710.all_reads G=1e8
GNU Make 4.3
Built for x86_64-conda-linux-gnu
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Reading makefiles...
Reading makefile '/opt/conda/envs/syri_env/bin/share/longstitch-1.0.3-0/longstitch'...
Updating makefiles....
@pmcarlton
pmcarlton / 2021-12-09_nematode_seq
Created December 9, 2021 07:39
sequence from M/F nematodes isolated from rotting pomegranate, 2021-11 in Kyoto University campus.
>N-2-PREMIX Length=602
NNNNNNNNACGNNNNCCCGCCNCCCGTACAGGATTTGCACCCTCTTCGATCTGTGGCCCCGCTCAAAGGGACTTCGGGTGGTGGAACGCGTCGGAAACCGACACCTATACGTCACATTTCCCAGCGACCATGGGCCGAGGGATTCGACGCTGGGCTTTTCCCCTTTCACTCGCCGTTACTGGGGGAATCTTCGTTAATTCCTTTTCCTCCGCTTAGTAATATGCTTAAGTTCAGCGGGTAATCACGACTGATCTGAGGTCTCTATTCGTTGGCACTTGGCGCGACGCCCGCGCTCGAACGTGATGATGAATATGAGAATATTATGCATCGCTCGAATCGGGCAAGCCGCAGTAAGCGTCAATGGCGATGTGCTGCTGCTGCTGCTGCAGCACATCATCGTTCGCCACGAGTCGAGCCAGCCACCCACCCACGAAAGGCAGGCGGCCAACACGAGCTCCCAGTAATCGCTGGATTTCACTCCGGGCAAAGTACATGTTTGCGGCCCTCATACNGACGTGCCGACGGNAAAACCCGCCGGCGCAATTTGCGTTCGAAATTTCNATGCTCANTGTGTNNGNNNTCNNNNNNNNAANNNNGNNNNN
@pmcarlton
pmcarlton / pmcarlton_napari-zelda-fix.diff
Created October 27, 2021 03:58
Fix for napari-zelda not having a "launch" option in the OSX menu
diff --git a/napari_zelda/napari_zelda.py b/napari_zelda/napari_zelda.py
index f6f6b6f..6479eca 100644
--- a/napari_zelda/napari_zelda.py
+++ b/napari_zelda/napari_zelda.py
@@ -33,7 +33,7 @@ def mock():
path=os.path.abspath(inspect.getfile(mock))
prot_path=os.path.dirname(os.path.dirname(path))
-protocols_file=open(prot_path+'\\napari_zelda'+'\protocols_dict.json', "rb")
+protocols_file=open(os.path.join(prot_path,'napari_zelda','protocols_dict.json'), "rb")
@pmcarlton
pmcarlton / pUC_lmnA_Neo_exn1_donor_fixed.gb
Created September 9, 2020 02:21
Sequence of pUC_lmnA_Neo_exn1_donor_fixed
LOCUS pUC_lmnA_Neo_exn 6027 bp ds-DNA circular 21-APR-2014
DEFINITION .
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 393..422
/label=30bp overlapping
@pmcarlton
pmcarlton / Bio-DB-HTS failing install log
Last active March 6, 2019 07:46
## Install Log
>> git clone https://github.com/Ensembl/Bio-DB-HTS.git
Cloning into 'Bio-DB-HTS'...
remote: Enumerating objects: 45, done.
remote: Counting objects: 100% (45/45), done.
remote: Compressing objects: 100% (29/29), done.
remote: Total 3693 (delta 17), reused 33 (delta 12), pack-reused 3648
Receiving objects: 100% (3693/3693), 9.98 MiB | 6.06 MiB/s, done.
Resolving deltas: 100% (1990/1990), done.
@pmcarlton
pmcarlton / bee_number_workflow.mkd
Last active June 11, 2018 01:11
Extract and calculate simple variance from target images, from DOI: 10.1126/science.aar4975
@pmcarlton
pmcarlton / mutt-sanitize-change
Last active January 10, 2018 08:28
removes safe_chars but replaces / and space with _
diff -ur a/a/lib.c b/b/lib.c
--- a/a/lib.c
+++ b/b/lib.c
@@ -705,7 +705,7 @@ void mutt_sanitize_filename (char *f, short slash)
for (; *f; f++)
{
- if ((slash && *f == '/'))
+ if (slash && *f == '/') || (*f == ' ')
*f = '_';
@pmcarlton
pmcarlton / all-wormbase-files.txt
Created November 10, 2017 06:57
This file has been truncated, but you can view the full file.
# this is a list of all files on the wormbase public server, as of 2017-11-02
# created using the "find" command of lftp
# 20171102pmc
./
./pub/
./pub/wormbase/
./pub/wormbase/README
./pub/wormbase/archive/
./pub/wormbase/archive/genomes/