PRINSEQ-GRAPHS-NOPCA(1)

💖 PRINSEQ-GRAPHS-NOPCA 💖

okay bestie, welcome to the PRINSEQ-GRAPHS-NOPCA(1) manual page, the group chat where we talk about making pretty graphs from your sequence data ✨

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🌸 NAME 🌸

PRINSEQ — which stands for PReprocessing and INformation of SEQuence data 🧬

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🎀 VERSION 🎀

PRINSEQ-graphs 0.6 — yes she's an icon, yes she's been around 💅

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✨ SYNOPSIS ✨

perl prinseq-graphs.pl [-h] [-help] [-version] [-man] [-verbose] [-i
input_graph_data_file] [-png_all] [-html_all] [-log file]

that's the whole vibe in one line, no cap 🫶

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🦋 DESCRIPTION 🦋

so basically, PRINSEQ is here to help you preprocess your genomic or metagenomic sequence data in FASTA (and QUAL) or FASTQ format 🌈

and this specific flavor, the graphs version? it lets users of the lite version generate graphs that look just like the ones from the web version 🎀 iconic behavior honestly.

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👑 OPTIONS 👑

💅 the basics

• -help | -h — prints the help message. that's it, that's the whole job. ignores every other argument you throw at it, she's not listening 💀
• -man — prints the full documentation. again, ignores other arguments, she said this is my moment 🙈
• -version — prints the program version. ignores other arguments too, she's committed to the bit.
• -verbose — prints status and info messages while processing, so you actually know what's going on instead of staring at a blank terminal 😭

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🌸 * INPUT OPTIONS * 🌸

• -i <file> — the input file containing the graph data, the one generated by the lite version. this is your raw material bestie, feed her 🍓

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🎀 * OUTPUT OPTIONS * 🎀

• -o <string> — so by default, output files get created in the same directory as the input file, with an extra _prinseq_graphs_XXXX tacked onto their name (where XXXX gets replaced by random characters, so you never overwrite your old files, she's thoughtful like that 💖). wanna change the output filename and location? just specify the filename with this option. the file extension gets added automatically, don't worry about it ✨
• -png_all — use this option to generate PNG files with the graphs 🖼️
• -html_all — use this option to generate an HTML file with the graphs and tables 📊
• -log <file> — log file to keep track of parameters, errors, etc. the log file name is optional 👀 if you don't give a file name, the log file name will be inputname.log. and if the log file already exists, new content gets added to the file (she appends, she doesn't overwrite, queen behavior 👑)

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💜 AUTHOR 💜

Robert SCHMIEDER, "<rschmieder_at_gmail_dot_com>" — the main character who made all this happen 🫶

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💀 BUGS 💀

if you find a bug please email me at "<rschmieder_at_gmail_dot_com>" or use http://sourceforge.net/tracker/?group_id=315449 so that I can make PRINSEQ better 🙏 fr fr, report the bugs, we're all growing together 🌱

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⭐ COPYRIGHT ⭐

Copyright (C) 2011-2012 Robert SCHMIEDER

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🌈 LICENSE 🌈

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

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ok and that's the whole page bestie, you made it to the end, proud of you 🥹💖

manual page PRINSEQ-GRAPHS-NOPCA(1), perl v5.32.0, dated 2020-11-09 — yeah she's vintage but she ate and left no crumbs 💅✨