PairSeq

Sorts and matches sequence records with matching coordinates across files

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

show program’s version number and exit

-h, --help

show this help message and exit

-1 <seq_files_1>

An ordered list of FASTA/FASTQ files containing head/primary sequences.

-2 <seq_files_2>

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

--fasta

Specify to force output as FASTA rather than FASTQ.

--failed

If specified create files containing records that fail processing.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--outdir <out_dir>

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.

--outname <out_name>

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.

--1f <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.

--2f <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.

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

The format of the sequence identifier which defines shared coordinate information across mate pairs.

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.