GTHGETSEQ(1)

✨ GTHGETSEQ(1) — the manual page bestie 💅

okay so this is the man page for gthgetseq, which lives in the GenomeThreader manual, section 1. pull up a chair, we're extracting sequences 🧬✨

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🌸 NAME 🌸

gthgetseq — get FASTA sequences from GenomeThreader files

🎀 SYNOPSIS 🎀

gthgetseq -getcdna | -getprotein | -getgenomic [option ...] [file ...]

🦋 DESCRIPTION 🦋

so basically, gthgetseq pulls FASTA sequences out of GenomeThreader files that are holding intermediate results. and where do those sequences go? straight to stdout, bestie. no files, no drama, just vibes on your terminal 💖

👑 OPTIONS 👑

okay here's the whole menu, no skips, no skimming, we read every single one 🌈

• -getcdna — get cDNA/EST sequences. default: no
• -getcdnacomp — get the complement of cDNA/EST sequences. default: no
• -getprotein — get protein sequences. default: no
• -getproteincomp — get the complement of protein sequences. default: no
• -getgenomic — get genomic sequences. default: no
• -getgenomiccomp — get the complement of genomic sequences. default: no
• -minalignmentscore — set the minimum alignment score for spliced alignments to be included into the set of spliced alignments. default: 0.00
• -maxalignmentscore — set the maximum alignment score for spliced alignments to be included into the set of spliced alignments. default: 1.00
• -mincoverage — set the minimum coverage for spliced alignments to be included into the set of spliced alignments. default: 0.00
• -maxcoverage — set the maximum coverage for spliced alignments to be included into the set of spliced alignments. default: 9999.99
• -gzip — gzip compressed input file(s). default: no
• -bzip2 — bzip2 compressed input file(s). default: no
• -help — display help and exit 🫶
• -version — display version information and exit ⭐

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quick vibe check: the three "get" flags in the synopsis are written with | between them — that's the shape of the command line as the page shows it, so keep it exactly like that. and yeah, every one of those "default: no" flags really does default to no, so nothing gets fetched unless you ask, periodt 💅

and that's the whole page, no crumbs left. this was GTHGETSEQ(1) from the GenomeThreader manual, and the footer said GTHGETSEQ(1) too — so consider yourself signed off, bestie, you ate this 🎀🦋💖