vimalinx/bio-agent - Page 7

pair-to-bed

Use when you need to find overlaps between paired-end read intervals (BEDPE or BAM) and genomic features in BED, GFF, or VCF format.

pair-to-pair

Use when comparing two paired-end BEDPE files to find overlapping pairs. Requires -a and -b BEDPE input files.

phage-design

Use when working from the local Evo 2 `phage_gen` project to design or analyze bacteriophage genomes, competition assays, or Gibson assembly fragments.

phmmer

Use when searching one or more protein query sequences against a protein sequence database with HMMER's one-pass sequence-vs-sequence searcher.

plot-ampliconstats

Use when visualizing amplicon sequencing statistics from samtools ampliconstats output, generating heatmaps and graphs for coverage and read analysis.

plot-bamstats

Use when visualizing `samtools stats` output as BAM QC plots, including merged reports and reference-GC-aware summaries.

plot-roh-py

Use when plotting runs of homozygosity from `run-roh.pl` style output directories into PNG tracks, optionally filtered by region, sample list, or group contrast.

plot-vcfstats

Use when converting `bcftools stats` output into variant-QC plots, per-sample PNG panels, and optional PDF summaries.

pma2apa

Use when converting `PubmedArticle` XML from EDirect into APA-style citation text or APA-structured XML for downstream parsing.

pma2pme

Use when converting `PubmedArticle` XML into `Pubmed-entry` ASN.1 text, or into the intermediate XML form used before final ASN.1 emission.

pmc2bioc

Use when converting PubMed Central article XML into BioC collection XML for downstream text-mining or annotation pipelines.

pmc2info

Use when converting PubMed Central article XML into normalized PMCInfo XML for local archive building or section-aware downstream parsing.

popt

Use when filtering `RNAsubopt -s` output to keep p-optimal RNA structures in a ViennaRNA post-processing pipeline.

print-columns

Use when projecting or transforming tab-delimited stdin columns with a tiny EDirect `awk` wrapper, especially for quick field arithmetic, quoting, or date stamping in shell pipelines.

print-missing-subranges

Use when reporting gaps in an ordered list of ascending integer positions, identifiers, or coordinates by printing the missing ranges between observed values.

prodigal

Use when predicting protein-coding genes in prokaryotic genomes or metagenomic sequences

project-tree-builder

Use when generating or dry-running NCBI-style Unix C++ project trees with `project_tree_builder`.

propmapped

Use when you need to calculate the proportion of mapped reads or fragments from SAM/BAM alignment files to assess mapping quality and success rates.

protein-structure

Use when planning or staging protein-structure prediction or structure-design work in this workspace, especially when deciding between missing local predictors and the repos that are actually present.

psiblast

Use when detecting distant protein homologs via iterative profile-based searches, building position-specific scoring matrices (PSSMs), or refining sequence similarity searches beyond standard BLASTP.

psl2sam-pl

Use when converting UCSC PSL alignments into SAM and controlling the simple alignment score calculation.

qualfa2fq-pl

Use when merging a legacy FASTA file and matching QUAL file into FASTQ, including `.gz` inputs, before downstream alignment or QC steps.

quality-scores

Use when sampling per-base Phred quality values from FASTQ, gzipped FASTQ, BAM, or SAM files via the Subread `qualityScores` utility.

quote-grouped-elements

Use when converting space-separated grouped values into quoted comma-joined lines for downstream EDirect or shell formatting steps.

random-bed

Use when generating random genomic intervals for simulation, background sets, or statistical testing.

rchive-linux

Use when calling the Linux-specific compiled `rchive.Linux` binary directly to build, query, or manage local XML archives and postings indices.

rchive

Use when building, indexing, or querying local XML record archives from NCBI Entrez databases, creating inverted indices, or managing PubMed local caches.

ref-cache

Use when managing local reference sequence caches for htslib-based tools. Invokes the ref-cache CLI to configure or interact with reference cache directories.

ref2pmid

Use when converting reference citations or identifiers to PubMed IDs (PMIDs) using Entrez Direct utilities.

refseq-nm-cds

Use when retrieving RefSeq NM coding sequences for supported species (cow, frog, human, mouse, pig, rat, zebrafish) via the entrez-direct toolkit.

remove-dup

Use when removing duplicate alignments from SAM or BAM files with the Subread `removeDup` CLI and a location-count cutoff.

reorder-columns

Use when you need to reorder columns in tabular bioinformatics data files while preserving row content.

repair

Use when paired-end reads need to be reordered so mates appear consecutively, or when preparing BAM files for featureCounts by adding dummy reads for singletons.

rfdiffusion

Use when working from the local RFdiffusion repository to generate protein backbones or binder designs through its Docker Compose workflows.

rna2-dfold

Use when computing MFE structures, partition functions, and Boltzmann-sampled secondary structures within k,l distance neighborhoods relative to two reference structures for an RNA sequence.

rnaaliduplex

Use when predicting conserved RNA-RNA interactions between two CLUSTAL alignments to identify evolutionary conserved binding sites, hybridization energies, and duplex structures.

rnaalifold

Use when predicting consensus secondary structures from multiple sequence alignments of RNA. Computes minimum free energy structures, partition functions, and base pairing probabilities for aligned RNA sequences.

rnacofold

Use when predicting secondary structures of two RNA sequences with dimerization, computing equilibrium concentrations of monomer and dimer species, or analyzing RNA-RNA hybridization thermodynamics.

rnaconsensus

Use when predicting RNA secondary structures for single sequences using information from multiple sequence alignments of homologous sequences.

rnadistance

Use when calculating distances between RNA secondary structures, including base pair distance and tree or string editing-based dissimilarity measures.