---
name: "CollapseSeq.py"
section: "1"
platform: "linux"
package: "presto"
version: "0.7.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/CollapseSeq.py"
---

# CollapseSeq.py(1)

emoves duplicate sequences from FASTA/FASTQ files

## NAME

CollapseSeq.py - emoves duplicate sequences from FASTA/FASTQ files

## DESCRIPTION

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} \[{min,max,sum,set} ...\]\] \[--inner\] \[--keepmiss\] \[--maxf MAX\_FIELD \| **--minf** MIN\_FIELD\]

Removes duplicate sequences from FASTA/FASTQ files

### help:

- **--version**

  show program's version number and exit

- **-h**, **--help**

  show this help message and exit

### standard arguments:

- **-s** SEQ\_FILES \[SEQ\_FILES ...\]

  A list of FASTA/FASTQ files containing sequences to process. (default: None)

- **-o** OUT\_FILES \[OUT\_FILES ...\]

  Explicit output file name(s). Note, this argument cannot be used with the **--failed**, **--outdir**, or **--outname** arguments. If unspecified, then the output filename will be based on the input filename(s). (default: None)

- **--outdir** OUT\_DIR

  Specify to changes the output directory to the location specified. The input file directory is used if this is not specified. (default: None)

- **--outname** OUT\_NAME

  Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files. (default: None)

- **--log** LOG\_FILE

  Specify to write verbose logging to a file. May not be specified with multiple input files. (default: None)

- **--failed**

  If specified create files containing records that fail processing. (default: False)

- **--fasta**

  Specify to force output as FASTA rather than FASTQ. (default: None)

- **--delim** DELIMITER DELIMITER DELIMITER

  A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively. (default: ('\|', '=', ','))

### collapse arguments:

- **-n** MAX\_MISSING

  Maximum number of missing nucleotides to consider for collapsing sequences. A sequence will be considered undetermined if it contains too many missing nucleotides. (default: 0)

- **--uf** UNIQ\_FIELDS \[UNIQ\_FIELDS ...\]

  Specifies a set of annotation fields that must match for sequences to be considered duplicates. (default: None)

- **--cf** COPY\_FIELDS \[COPY\_FIELDS ...\]

  Specifies a set of annotation fields to copy into the unique sequence output. (default: None)

- **--act** {min,max,sum,set} \[{min,max,sum,set} ...\]

  List of actions to take for each copy field which defines how each annotation will be combined into a single value. The actions "min", "max", "sum" perform the corresponding mathematical operation on numeric annotations. The action "set" collapses annotations into a comma delimited list of unique values. (default: None)

- **--inner**

  If specified, exclude consecutive missing characters at either end of the sequence. (default: False)

- **--keepmiss**

  If specified, sequences with more missing characters than the threshold set by the **-n** parameter will be written to the unique sequence output file with a DUPCOUNT=1 annotation. If not specified, such sequences will be written to a separate file. (default: False)

- **--maxf** MAX\_FIELD

  Specify the field whose maximum value determines the retained sequence; mutually exclusive with **--minf**. (default: None)

- **--minf** MIN\_FIELD

  Specify the field whose minimum value determines the retained sequence; mutually exclusive with **--minf**. (default: None)

### output files:

-

  collapse-unique

-

  unique sequences. Contains one representative from each set of duplicate sequences. The retained representative is determined by user defined criteria.

-

  collapse-duplicate

-

  raw reads which are duplicates of the sequences retained in the collapse-unique file.

-

  collapse-undetermined

-

  raw reads which were excluded from consideration due to having too many N characters in the sequence.

### output annotation fields:

-

  DUPCOUNT

-

  total number of sequences within the set of duplicates for each retained unique sequence. Meaning, the copy number of each unique sequence within the data file.

-

  \<user defined\>

-

  annotation fields specified by the **--cf** parameter.

## AUTHOR

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