PRINSEQ-GRAPHS(1)

💖 PRINSEQ-GRAPHS 💖

okay so bestie, welcome to prinseq-graphs — that's section 1 of the manual, the one you pull up when you're like "wait how do I make pictures out of this". it's the graphing bestie of PRINSEQ, no cap. she's a perl script and she's ready to serve. ✨

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🌸 NAME 🌸

PRINSEQ — aka PReprocessing and INformation of SEQuence data. yes it's an acronym, yes it's iconic, we love a recursive naming moment. 💅

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🎀 VERSION 🎀

PRINSEQ-graphs 0.6 — she's version 0.6 and she's thriving. 🦋

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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 right there. run her with perl, feed her some graph data, get visuals. periodt. 👑

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🫶 DESCRIPTION 🫶

PRINSEQ is here to help you preprocess your genomic or metagenomic sequence data — and she does it in FASTA (plus QUAL) or FASTQ format, whatever your little heart desires. 💖

so here's the tea: the graphs version exists so that the lite version girlies can generate graphs similar to the web version. you don't need the website, you don't need to be online, you just need this script and a dream. lowkey revolutionary of her. 🌈

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💅 OPTIONS 💅

okay this is the part you actually came for. read every single one, don't skip, I will know. 🙈

• -help | -h — prints the help message and dips. she ignores every other argument you threw at her, so don't bother being extra. 😌
• -man — prints the full documentation and also ignores all your other arguments. this is the "give me the whole lore" option. 📖
• -version — prints the program version. ignores other arguments too. she's brief and she's booked. ✨
• -verbose — prints status and info messages while she's processing. use this if you're nosy (affectionate) and want to watch her work. 👀

***** INPUT OPTIONS *****

• -i <file> — the input file containing the graph data generated by the lite version. this is the snack you're feeding her. 🍓

***** OUTPUT OPTIONS *****

• -o <string> — by default, the 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 swapped out for random characters, so you never accidentally overwrite your previous files — she's thoughtful like that 🥹). if you wanna change the output filename and location, just specify the filename with this option. the file extension will be added automatically, so don't stress about it. 💅
• -png_all — use this to generate PNG files with the graphs. pictures!! actual pictures!! 📸
• -html_all — use this to generate an HTML file with the graphs and tables. the whole package, the full main character moment. 🌟
• -log <file> — log file to keep track of parameters, errors, etc. the log file name is optional! if you don't give her a file name, the log file name will be "inputname.log". and heads up — if the log file already exists, the new content gets added to the file, it doesn't get wiped. so she's an accumulator, she keeps receipts. 📝

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👑 AUTHOR 👑

Robert SCHMIEDER, "<rschmieder_at_gmail_dot_com>". legend behaviour, honestly. 🫡

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💀 BUGS 💀

if you find a bug, please email him at "<rschmieder_at_gmail_dot_com>" or use http://sourceforge.net/tracker/?group_id=315449 so that he can make PRINSEQ better. bestie really said "tell me everything, I want to grow". 😭💖

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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. slay, freedom of the code. 💜

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/.

ngl the all-caps warranty disclaimer is giving "not responsible for your situationship" energy but make it legal. read it, it matters. 🚨

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and that's the whole page, bestie!! this one was documented with perl v5.32.0 and dated 2020-11-09, and she's still out here graphing. go make something pretty. 💖✨🎀