PAIRSEQ.PY(1)

🎀 PAIRSEQ.PY(1) 🎀

bestie, this is the User Commands page for PairSeq.py 🦋

✨ NAME ✨

PairSeq.py, okay so it sorts and matches sequence records that have matching coordinates across files 💖

🦋 DESCRIPTION 🦋

Here's the usage line, copy-paste it exactly 💅

usage: PairSeq.py [--version] [-h] -1 SEQ_FILES_1 [SEQ_FILES_1 ...] -2
SEQ_FILES_2 [SEQ_FILES_2 ...] [--outdir OUT_DIR] [--outname OUT_NAME]
[--failed] [--fasta] [--delim DELIMITER DELIMITER DELIMITER]
[--1f FIELDS_1 [FIELDS_1 ...]] [--2f FIELDS_2 [FIELDS_2 ...]]
[--act {min,max,sum,set,cat}] [--coord {illumina,solexa,sra,454,presto}]

So basically, it sorts and matches sequence records with matching coordinates across files. Main character energy 👑

🌸 help

• --version — the program flexes its version number and then bounces 👋
• -h, --help — pulls up the help message and then exits 🙈

🍓 standard arguments

• -1 SEQ_FILES_1 [SEQ_FILES_1 ...] — an ordered list of FASTA/FASTQ files holding the head/primary sequences. (default: None)
• -2 SEQ_FILES_2 [SEQ_FILES_2 ...] — an ordered list of FASTA/FASTQ files holding the tail/secondary sequences. (default: None)
• --outdir OUT_DIR — changes the output directory to the location you give. If you skip this, the input file's directory gets used instead. (default: None)
• --outname OUT_NAME — swaps the prefix of the successfully processed output file for whatever string you pass. > You can't use this with multiple input files, bestie 💀 (default: None)
• --failed — if you add this, it creates files full of the records that fail processing. (default: False)
• --fasta — forces the output to be FASTA instead of FASTQ, no debate 🧚 (default: None)
• --delim DELIMITER DELIMITER DELIMITER — three delimiters, in order: the ones that separate annotation blocks, the ones between field names and values, and the ones between values within a field. (default: ('|', '=', ','))

🦋 pairing arguments

• --1f FIELDS_1 [FIELDS_1 ...] — the annotation fields you want copied from file 1 records into file 2 records. If an annotation you copied is already in a file 2 record, the file 1 annotations get stuck on the front of the existing one 🫶 (default: None)
• --2f FIELDS_2 [FIELDS_2 ...] — the annotation fields you want copied from file 2 records into file 1 records. If an annotation you copied is already in a file 1 record, the file 2 annotations get tacked onto the end of the existing one ✨ (default: None)
• --act {min,max,sum,set,cat} — the collapse actions for combining duplicate copied fields into one value 🔥
  • min, max, and sum do the matching math on numeric annotations.
  • set squishes the annotations into a comma-delimited list of unique values.
  • cat glues the values together into one single string.
  • This only kicks in if the field was already in the header before getting copied over from the other file. (default: None)
• --coord {illumina,solexa,sra,454,presto} — the format of the sequence identifier that defines the shared coordinate info across mate pairs. (default: presto)

🧚 output files

• pair-pass — successfully paired reads, with their annotations all glowed up 🌈
• pair-fail — raw reads that couldn't get assigned a mate-pair 💀

🎀 output annotation fields

• <user defined> — the annotation fields you picked with the --1f or --2f arguments 💜

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. Iconic behaviour from Andreas 🫶

Okay that's the whole page, bestie 💖 It's PairSeq.py 0.6.0, dated May 2020, and it lives on as PAIRSEQ.PY(1) 🌸 Now go match some sequences and slay 💅✨