vimalinx/bio-agent - 第 11 页

windowmasker

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

原文语言：英语

word-at-a-time

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

原文语言：英语

xa2multi-pl

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

原文语言：英语

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.

原文语言：英语

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.

原文语言：英语

xfilter

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

原文语言：英语

xinfo

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

原文语言：英语

xlink

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

原文语言：英语

xml2fsa

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

原文语言：英语

xml2json

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

原文语言：英语

xml2tbl

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

原文语言：英语

xsearch

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

原文语言：英语

xtract-linux

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

原文语言：英语

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…

原文语言：英语

yaml2xml

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

原文语言：英语

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.

原文语言：英语

zoom2sam-pl

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

原文语言：英语