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.