PairSeq.py

Sorts and matches sequence records with matching coordinates across files

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}]

--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.

--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.

--failed

If specified create files containing records that fail processing.

--fasta

Specify to force output as FASTA rather than FASTQ.

--delim <delimiter>

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

--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.

--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.

--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.