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

# PairSeq.py(1)

Sorts and matches sequence records with matching coordinates across files

## NAME

PairSeq.py - Sorts and matches sequence records with matching coordinates across files

## DESCRIPTION

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 \[FIELDS\_2 ...\]\] \[--act {min,max,sum,set,cat}\] \[--coord {illumina,solexa,sra,454,presto}\]

Sorts and matches sequence records with matching coordinates across files

### help:

- **--version**

  show program's version number and exit

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

  show this help message and exit

### standard arguments:

- **-1** SEQ\_FILES\_1 \[SEQ\_FILES\_1 ...\]

  An ordered list of FASTA/FASTQ files containing head/primary sequences. (default: None)

- **-2** SEQ\_FILES\_2 \[SEQ\_FILES\_2 ...\]

  An ordered list of FASTA/FASTQ files containing tail/secondary sequences. (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)

- **--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: ('\|', '=', ','))

### pairing arguments:

- **--1f** FIELDS\_1 \[FIELDS\_1 ...\]

  The annotation fields to copy from file 1 records into file 2 records. If a copied annotation already exists in a file 2 record, then the annotations copied from file 1 will be added to the front of the existing annotation. (default: None)

- **--2f** FIELDS\_2 \[FIELDS\_2 ...\]

  The annotation fields to copy from file 2 records into file 1 records. If a copied annotation already exists in a file 1 record, then the annotations copied from file 2 will be added to the end of the existing annotation. (default: None)

- **--act** {min,max,sum,set,cat}

  The collapse actions to take on all fields copied between files to combine duplicate fields 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. The action "cat" concatenates the values together into a single string. Only applies if the field already exists in the header before being copying from the other file. (default: None)

- **--coord** {illumina,solexa,sra,454,presto}

  The format of the sequence identifier which defines shared coordinate information across mate pairs. (default: presto)

### output files:

-

  pair-pass

-

  successfully paired reads with modified annotations.

-

  pair-fail

-

  raw reads that could not be assigned to a mate-pair.

### output annotation fields:

-

  \<user defined\>

-

  annotation fields specified by the **--1f** or **--2f** arguments.

## AUTHOR

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