How do I install the Seq Cache Populate Pl skill?

Run npx skillmds add vimalinx/seq-cache-populate-pl in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Is Seq Cache Populate Pl free to use?

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Who published Seq Cache Populate Pl?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Seq Cache Populate Pl by vimalinx — Agent Skill

Name: Seq Cache Populate Pl
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

seq-cache-populate-pl

Perl cache builder for htslib reference caching. It reads FASTA entries, uppercases and whitespace-strips the sequence, hashes the normalized sequence by MD5, and writes each entry into a REF_CACHE-style directory tree under the chosen root.

Quick Start

Command: seq_cache_populate.pl -root <dir> input1.fasta ...
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/seq_cache_populate.pl
Main output: populated cache tree plus a printed REF_CACHE=... template

When To Use This Tool

Building a CRAM-compatible reference cache from FASTA files
Precomputing MD5-keyed reference paths before samtools, htslib, or CRAM workflows
Scanning a directory tree for FASTA-like files with -find
Reusing an existing cache root and skipping entries that are already present

Common Patterns

# Populate a cache from one FASTA file
seq_cache_populate.pl -root ref_cache reference.fa

# Scan a directory tree for FASTA-like files
seq_cache_populate.pl -root ref_cache -find refs/

# Use a deeper hash directory layout
seq_cache_populate.pl -root ref_cache -subdirs 15 reference.fa

Recommended Workflow

Pick a cache root that downstream CRAM tools can read consistently.
Choose direct FASTA arguments, -find <dir>, or stdin if you want to stream one FASTA file through the script.
Run the script and capture the printed REF_CACHE=... template.
Export that REF_CACHE value in later samtools / htslib jobs that need reference lookup by MD5.

Guardrails

-root <dir> is mandatory. With no arguments, the script prints only the usage banner.
The tool is a normal Perl script, so its only built-in usage path is the Perl GetOptions failure / missing-argument banner; there is no separate --version.
Live testing showed cache entries created under MD5-derived hex paths such as cache/f1/f8/f4bf..., followed by a printed Use environment REF_CACHE=.../%2s/%2s/%s.
Re-running against the same FASTA does not duplicate entries; it prints Already exists: <md5> <seqid> instead.
-find only accepts candidate files whose first line looks like >id and whose second line matches a nucleotide alphabet regex.
Source inspection shows -subdirs 16 is rejected, but the error text misleadingly says it “should be less than 15”; local testing confirmed -subdirs 15 still works.
Large sequences spill to temporary files once buffered sequence length exceeds roughly 256 MiB, and those temporary files are created under the chosen cache root.

---name: seq-cache-populate-pldescription: Use when populating an htslib/CRAM `REF_CACHE` directory from FASTA input or by scanning a directory tree for FASTA files.--- # seq-cache-populate-pl Perl cache builder for htslib reference caching. It reads FASTA entries, uppercases and whitespace-strips the sequence, hashes the normalized sequence by MD5, and writes each entry into a `REF_CACHE`-style directory tree under the chosen root. ## Quick Start - **Command:** `seq_cache_populate.pl -root <dir> input1.fasta ...` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/seq_cache_populate.pl` - **Main output:** populated cache tree plus a printed `REF_CACHE=...` template ## When To Use This Tool - Building a CRAM-compatible reference cache from FASTA files - Precomputing MD5-keyed reference paths before `samtools`, `htslib`, or CRAM workflows - Scanning a directory tree for FASTA-like files with `-find` - Reusing an existing cache root and skipping entries that are already present ## Common Patterns ```bash # Populate a cache from one FASTA file seq_cache_populate.pl -root ref_cache reference.fa ``` ```bash # Scan a directory tree for FASTA-like files seq_cache_populate.pl -root ref_cache -find refs/ ``` ```bash # Use a deeper hash directory layout seq_cache_populate.pl -root ref_cache -subdirs 15 reference.fa ``` ## Recommended Workflow 1. Pick a cache root that downstream CRAM tools can read consistently. 2. Choose direct FASTA arguments, `-find <dir>`, or stdin if you want to stream one FASTA file through the script. 3. Run the script and capture the printed `REF_CACHE=...` template. 4. Export that `REF_CACHE` value in later `samtools` / `htslib` jobs that need reference lookup by MD5. ## Guardrails - `-root <dir>` is mandatory. With no arguments, the script prints only the usage banner. - The tool is a normal Perl script, so its only built-in usage path is the Perl `GetOptions` failure / missing-argument banner; there is no separate `--version`. - Live testing showed cache entries created under MD5-derived hex paths such as `cache/f1/f8/f4bf...`, followed by a printed `Use environment REF_CACHE=.../%2s/%2s/%s`. - Re-running against the same FASTA does not duplicate entries; it prints `Already exists: <md5> <seqid>` instead. - `-find` only accepts candidate files whose first line looks like `>id` and whose second line matches a nucleotide alphabet regex. - Source inspection shows `-subdirs 16` is rejected, but the error text misleadingly says it “should be less than 15”; local testing confirmed `-subdirs 15` still works. - Large sequences spill to temporary files once buffered sequence length exceeds roughly `256 MiB`, and those temporary files are created under the chosen cache root.

Frequently asked questions