COLLAPSESEQ.PY(1)

✨ NAME ✨

CollapseSeq.py 💖 is the duplicate-sequence remover for FASTA/FASTQ files, and it removes duplicate sequences from them. 🧹✨

💅 DESCRIPTION 💅

Okay so here's the synopsis, bestie:

usage: CollapseSeq.py [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
       [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
       [--outname OUT_NAME] [--log LOG_FILE] [--failed] [--fasta]
       [--delim DELIMITER DELIMITER DELIMITER] [-n MAX_MISSING] [--uf
       UNIQ_FIELDS [UNIQ_FIELDS ...]]  [--cf COPY_FIELDS [COPY_FIELDS
       ...]]  [--act {min,max,sum,set} [{min,max,sum,set} ...]]
       [--inner] [--keepmiss] [--maxf MAX_FIELD | --minf MIN_FIELD]

It's giving duplicate removal realness: it removes duplicate sequences from FASTA/FASTQ files. 🦋

🌸 help:

• --version — shows the program's version number and then exits. ✨
• -h, --help — shows the help message and exits. 💜

🎀 standard arguments:

• -s SEQ_FILES [SEQ_FILES ...] — the list of FASTA/FASTQ files holding the sequences you want processed. (default: None) 🍓
• -o OUT_FILES [OUT_FILES ...] — explicit output file name(s). Heads up, this one cannot be used with --failed, --outdir, or --outname. If you don't set it, the output filename gets based on your input filename(s). (default: None) 🧚
• --outdir OUT_DIR — changes the output directory to the location you give it. If you don't specify one, the input file's directory gets used. (default: None) 📁
• --outname OUT_NAME — changes the prefix of the successfully processed output file to whatever string you pick. You can't use this with multiple input files. (default: None) 🌈
• --log LOG_FILE — writes verbose logging to a file. You can't use this with multiple input files. (default: None) 📝
• --failed — makes files holding the records that fail processing. (default: False) 💀
• --fasta — forces the output to be FASTA instead of FASTQ. (default: None) 🌸
• --delim DELIMITER DELIMITER DELIMITER — a list of the three delimiters, in order: the ones that separate annotation blocks, the ones that separate field names from values, and the ones that separate values within a field. (default: ('|', '=', ',')) 🫶

💜 collapse arguments:

• -n MAX_MISSING — the max number of missing nucleotides a sequence can have and still be considered for collapsing. If it has too many missing nucleotides, it's labelled undetermined. (default: 0) 🙈
• --uf UNIQ_FIELDS [UNIQ_FIELDS ...] — picks a set of annotation fields that must match for sequences to count as duplicates. 👯
• --cf COPY_FIELDS [COPY_FIELDS ...] — picks a set of annotation fields to copy into the unique sequence output. 📋
• --act {min,max,sum,set} [{min,max,sum,set} ...] — a list of actions, one for each copy field, that decides how each annotation gets combined 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. (default: None) 👑
• --inner — if you set this, consecutive missing characters at either end of the sequence get excluded. (default: False) 🦋
• --keepmiss — if you set this, sequences with more missing characters than the -n threshold still get written to the unique sequence output file, but with a DUPCOUNT=1 annotation. If you don't set it, those sequences go into a separate file instead. (default: False) 🔥
• --maxf MAX_FIELD — picks the field whose maximum value decides which sequence gets kept. This is mutually exclusive with --minf. (default: None) ⭐
• --minf MIN_FIELD — picks the field whose minimum value decides which sequence gets kept. This is mutually exclusive with --minf. (default: None) ⭐

🧚 output files:

• collapse-unique — the unique sequences! It holds one representative from each set of duplicates. The one that gets kept depends on the criteria you defined. 💖
• collapse-duplicate — the raw reads that are duplicates of the sequences kept in the collapse-unique file. 🌸
• collapse-undetermined — the raw reads that got excluded from consideration because they had too many N characters in the sequence. 💀

🌈 output annotation fields:

• DUPCOUNT — the total number of sequences in the set of duplicates for each retained unique sequence. Basically, the copy number of each unique sequence in the data file. 🍓
• <user defined> — the annotation fields you specified with the --cf parameter. 🎀

🫶 AUTHOR 🫶

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

Bye bestie! 🦋 CollapseSeq.py 0.6.0, May 2020 💅✨