FASTAQ-SEARCH_FOR_SEQ(1)

👑 NAME 👑

fastaq_search_for_seq — bestie, this finds every single exact match to a string and its reverse complement 🧬✨

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💖 DESCRIPTION 💖

okay so the vibe is: you give it a file, a string, and an output file, and it goes feral hunting for that string inside every sequence. Periodt.

Here's the usage line, verbatim, no notes:

usage: fastaq_search_for_seq [options] <infile> <outfile> <search_string>

So what's actually happening? It searches for an exact match on a given string and its reverse complement, in every sequence of the input sequence file. It's case insensitive (yes queen, ACGT and acgt are the same thing to her 💅). And it is guaranteed to find all hits — not some hits, not most hits, all of them. No cap. 🔥

🎀 positional arguments 🎀

• infile — the name of the input file. that's your source, your main character 🫶
• outfile — the name of the output file. and listen, the output is tab-delimited, with these three columns in this exact order: sequence name, position, strand. iconic formatting, we love a predictable layout 🌸
• search_string — the string you want it to search for in the sequences. go find your little pattern, bestie 🔍

✨ options ✨

• -h, --help — shows this help message and exits. the classic. the legend. always there when you need her 💜

quick reality check: no --version flag here, no extra flags hiding in the back, just -h/--help and the three positional args. the whole menu, fr fr.

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💀 if you forget an argument, she will not be happy. three positional args, in order: <infile> <outfile> <search_string>. don't improvise.

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🌈 SEE ALSO 🌈

nothing else listed, bestie — this one's a solo act 😭

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and that's the whole page!! this was fastaq_search_for_seq, version 3.17.0, dated January 2026 🎀 take care of her and she'll find every hit you ever dreamed of. mwah 💖🦋✨