vimalinx/bio-agent - Seite 11

windowmasker

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

Quellsprache: Englisch

word-at-a-time

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

Quellsprache: Englisch

xa2multi-pl

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

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.

Quellsprache: Englisch

xfilter

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

Quellsprache: Englisch

xinfo

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

Quellsprache: Englisch

xlink

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

Quellsprache: Englisch

xml2fsa

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

Quellsprache: Englisch

xml2json

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

Quellsprache: Englisch

xml2tbl

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

Quellsprache: Englisch

xsearch

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

Quellsprache: Englisch

xtract-linux

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

Quellsprache: Englisch

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…

Quellsprache: Englisch

yaml2xml

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

zoom2sam-pl

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

Quellsprache: Englisch