vimalinx/bio-agent - Page 11

windowmasker

Use when masking repetitive or low-complexity regions in genomic sequences before alignment or database searches

word-at-a-time

Use when tokenizing free text into lowercase one-word-per-line output by stripping non-alphanumeric separators.

xa2multi-pl

Use when expanding BWA `XA:Z` alternate-alignment tags in SAM records into separate secondary SAM alignments for downstream tools.

xcommon-sh

Use when reading or debugging the shared `xcommon.sh` shell library that supplies local-archive discovery, stdin parsing, and common helper functions to EDirect `x*` scripts.

xfetch

Use when retrieving records from a local EDirect archive via the `x*` local-cache stack, not when calling the remote NCBI `efetch` service directly.

xfilter

Use when filtering a UID stream against a local postings index with a query expression in the `x*` local-archive toolchain.

xinfo

Use when inspecting fields, indexed terms, or term counts from a local EDirect postings index rather than the remote `einfo` endpoint.

xlink

Use when following local EDirect link relations such as PubMed `CITED`, `CITES`, or `PMCID` from an incoming UID stream or `ENTREZ_DIRECT` message.

xml2fsa

Use when converting NCBI XML sequence records to FASTA format, typically after fetching data with efetch from the Entrez Direct toolkit.

xml2json

Use when converting XML documents into pretty-printed JSON for downstream parsing, provided the legacy Perl XML::Simple dependency is available.

xml2tbl

Use when extracting INSDSeq XML feature tables into tab-delimited text for downstream parsing or annotation review.

xsearch

Use when searching a local NCBI EDirect archive/postings index with Boolean, title, word, or pair queries inside the `x*` local-cache workflow.

xtract-linux

Use when calling the Linux-specific compiled `xtract.Linux` binary directly to extract tabular or XML output from structured XML records.

xtract

Use when parsing, extracting, or converting XML data from NCBI Entrez or other bioinformatics sources into tab-delimited tables. Use for selecting specific elements, filtering records, and restructuring hierarchical XML into flat formats for downstream…

yaml2xml

Use when converting YAML documents into XML for downstream EDirect or XML-based processing.

yeast-database

Use when working inside the local `yeast_genome_learning` project to download, validate, and analyze Saccharomyces cerevisiae reference data through its teaching scripts.

zoom2sam-pl

Use when converting legacy Zoom aligner output into SAM and the read length must be supplied explicitly.