TRANSIT-TPP(1)

💖 NAME 💖

transit-tpp — the girl who does statistical calculations of essentiality of genes or genomic regions. That's it, that's the job. She looks at your genes and is like "okay but which ones are actually essential" and then does math about it. 💅🧬

🌸 DESCRIPTION 🌸

Okay so here's the whole entire vibe of how you run her:

python PATH/src/tpp.py -bwa <EXECUTABLE_WITH_PATH> -ref <fasta-file|comma_separated_list> -reads1 <FASTQ_OR_FASTA_FILE> [-reads2 <FASTQ_OR_FASTA_FILE>] -output <BASE_FILENAME> [OPTIONAL ARGS]

Notice how -bwa, -ref, -reads1 and -output are the bare minimum, and -reads2 is chilling in brackets because she's optional, and then there's a whole [OPTIONAL ARGS] situation at the end for the rest of the girls. 🦋

✨ OPTIONAL ARGS ✨

Bestie, this is the fun part. Here's every single one, no skips, no cuts, we are not doing that today. 🎀

• -protocol [Sassetti|Tn5|Mme1] — which sample prep protocol was used? Yes, that's a question, she's asking you. The sassetti protocol is the default, and picking a protocol sets the default transposon and primer sequence for you. King behavior honestly. 👑
• -primer <seq> — this is the prefix of the reads that correspond to the end of the transposon, right at the junction with the genomic sequence. You can use this to override the default seq. She said "I'll pick one for you but you can absolutely do it yourself, main character." 🌟
• -maxreads <INT> — literally no description in the original, she just takes an INT and minds her business. 🙈
• -mismatches <INT> — this one's for when she's searching for constant regions in reads 1 and 2. The default is 1. 🔍
• -flags "<STRING>" — the args you want to pass straight to BWA. Note the quotes, keep the quotes, the quotes are load-bearing. 💀
• -bwa-alg [aln|mem] — which algorithm to use for mapping reads with bwa. Default: mem. Two choices only, aln or mem, she's not complicated. ⭐
• -primer-start-window INT,INT — the position in the read where she should search for the start of the primer. Default is [0,20]. Yes, two ints, comma between them, that's the format, don't fight it. 🧚
• -window-size INT — the automatic method to set window. 🪟✨
• -barseq_catalog_in|-barseq_catalog_out <file> — takes a <file>, that's all the original says, so that's all I'm saying. 🌈
• -replicon-ids <comma_separated_list_of_names> — if you gave her multiple replicons/genomes/contigs/sequences in -ref, this is where you give them names. And if you're feeling lazy? Enter 'auto' for autogenerated ids and let her handle it. 👑

🫶 Quick reminder for the girlies: keep every placeholder exactly as written — <EXECUTABLE_WITH_PATH>, <fasta-file|comma_separated_list>, <FASTQ_OR_FASTA_FILE>, <BASE_FILENAME> — because she reads them literally and so should you. No cap.

That's the whole page, bestie. Every flag, every default, every bracket, all of it, intact and iconic. 💖

Signing off the way she does: this is transit-tpp, version 3.1.0, dated August 2020. Slay forever, periodt. 💅🌸✨