Andrew Perry pansapiens

## sif2docker.sh
#!/bin/bash

set -euo pipefail

function show_usage() {
    echo "Usage: $0 <input.sif> [docker_image_name:tag]"
    echo
    echo "Converts a Apptainer/Singularity SIF file to a Docker image."
    echo
    echo "Arguments:"

## hmmer_tblout_parser.py
#!/usr/bin/env python
# MIT License
# Copyright (c) 2022 Zebulun Arendsee (rhmmer code)
# Copyright (c) 2025 Andrew Perry (port to Python)

# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is

## for-codes.tsv

          
            30
            AGRICULTURAL, VETERINARY AND FOOD SCIENCES

            
              3001
              Agricultural biotechnology

            
              300101
              Agricultural biotechnology diagnostics (incl. biosensors)

            
              300102
              Agricultural marine biotechnology

            
              300103
              Agricultural molecular engineering of nucleic acids and proteins

            
              300104
              Genetically modified animals

            
              300105
              Genetically modified field crops and pasture

            
              300106
              Genetically modified horticulture plants

            
              300107
              Genetically modified trees

            
              300108
              Livestock cloning

## ollama-export.sh
#!/bin/bash
# Ollama Model Export Script
# Usage: bash ollama-export.sh vicuna:7b
# License: MIT (https://ncurl.xyz/s/o_o6DVqIR)
# https://gist.github.com/supersonictw/f6cf5e599377132fe5e180b3d495c553

set -e

echo "Ollama Model Export Script"
echo "License: MIT (https://ncurl.xyz/s/RD0Yl5fSg)"

## appengine_leveldb2json.py
#!/usr/bin/env python2.7

# Export from Google App Engine Datastore Backup LevelDB format to JSON flat file
# Based on: https://gist.github.com/xlfe/af25f160256e4d52f499dee7e8fa212f

##
# 2024 instructions:
##
# Using the Google Cloud console (https://console.cloud.google.com), find "Firestore"
# and export your database to a Cloud Storage "Bucket". Download the content of the Bucket.

## bam2fq_softclip.py
#!/usr/bin/env python

###
# bam2fq_softclip.py
###
# A script for exploring soft-clipping of aligned reads.
# Extracts mapped reads from a BAM file as a FASTQ, but encodes 'soft-clipped' regions
# as lowercase. Soft-clipped regions can be quickly visualized in the terminal like:
#
# ./bam2fq_softclip.py aligned.bam | grep --color=always [atcg] |less -R

## .a_README.md

      
              4 files
            
          
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                pansapiens
                / .a_README.md
            
            
              Last active
              June 13, 2024 03:25
            
              
                schollz/hostyoself docker-compose
              
          
    A simple Docker Compose recipe for schollz/hostyoself.

  
## mirdeep_csv_to_counts.py
#!/usr/bin/env python

import argparse
import pandas as pd
import re
import sys
from typing import Optional, List
import logging
import glob
import io

## find_adapters.sh
#!/bin/bash

# Given a directory of fastq files, use bbmerge to find adapters sequences for every sample,
# align and find the consensus.
# Final consensus is in  r1_adapter.consensus.fa and r2_adapter.consensus.fa - trim by hand
# if the automatic trimming up the the first 'n' isn't sensible

# Requires: bbmerge.sh (bbmap), muscle, emboss (cons)


## R-kill-vscode-remote.sh
#!/bin/bash

R_TMUX_SESSION_NAME="${R_TMUX_SESSION_NAME:-vscode-r}"
TMUX_CMD=$(command -v tmux)

if ! [ -x "$(command -v tmux)" ]; then
    echo "Error: tmux is not installed."
    exit 1
fi
	#!/bin/bash

	set -euo pipefail

	function show_usage() {
	echo "Usage: $0 <input.sif> [docker_image_name:tag]"
	echo
	echo "Converts a Apptainer/Singularity SIF file to a Docker image."
	echo
	echo "Arguments:"
	#!/usr/bin/env python
	# MIT License
	# Copyright (c) 2022 Zebulun Arendsee (rhmmer code)
	# Copyright (c) 2025 Andrew Perry (port to Python)

	# Permission is hereby granted, free of charge, to any person obtaining a copy
	# of this software and associated documentation files (the "Software"), to deal
	# in the Software without restriction, including without limitation the rights
	# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
	# copies of the Software, and to permit persons to whom the Software is
	30	AGRICULTURAL, VETERINARY AND FOOD SCIENCES
	3001	Agricultural biotechnology
	300101	Agricultural biotechnology diagnostics (incl. biosensors)
	300102	Agricultural marine biotechnology
	300103	Agricultural molecular engineering of nucleic acids and proteins
	300104	Genetically modified animals
	300105	Genetically modified field crops and pasture
	300106	Genetically modified horticulture plants
	300107	Genetically modified trees
	300108	Livestock cloning
	#!/bin/bash
	# Ollama Model Export Script
	# Usage: bash ollama-export.sh vicuna:7b
	# License: MIT (https://ncurl.xyz/s/o_o6DVqIR)
	# https://gist.github.com/supersonictw/f6cf5e599377132fe5e180b3d495c553

	set -e

	echo "Ollama Model Export Script"
	echo "License: MIT (https://ncurl.xyz/s/RD0Yl5fSg)"
	#!/usr/bin/env python2.7

	# Export from Google App Engine Datastore Backup LevelDB format to JSON flat file
	# Based on: https://gist.github.com/xlfe/af25f160256e4d52f499dee7e8fa212f

	##
	# 2024 instructions:
	##
	# Using the Google Cloud console (https://console.cloud.google.com), find "Firestore"
	# and export your database to a Cloud Storage "Bucket". Download the content of the Bucket.
	#!/usr/bin/env python

	###
	# bam2fq_softclip.py
	###
	# A script for exploring soft-clipping of aligned reads.
	# Extracts mapped reads from a BAM file as a FASTQ, but encodes 'soft-clipped' regions
	# as lowercase. Soft-clipped regions can be quickly visualized in the terminal like:
	#
	# ./bam2fq_softclip.py aligned.bam \| grep --color=always [atcg] \|less -R
	#!/usr/bin/env python

	import argparse
	import pandas as pd
	import re
	import sys
	from typing import Optional, List
	import logging
	import glob
	import io
	#!/bin/bash

	# Given a directory of fastq files, use bbmerge to find adapters sequences for every sample,
	# align and find the consensus.
	# Final consensus is in r1_adapter.consensus.fa and r2_adapter.consensus.fa - trim by hand
	# if the automatic trimming up the the first 'n' isn't sensible

	# Requires: bbmerge.sh (bbmap), muscle, emboss (cons)
	#!/bin/bash

	R_TMUX_SESSION_NAME="${R_TMUX_SESSION_NAME:-vscode-r}"
	TMUX_CMD=$(command -v tmux)

	if ! [ -x "$(command -v tmux)" ]; then
	echo "Error: tmux is not installed."
	exit 1
	fi