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}]
Sorts and matches sequence records with matching coordinates
across files
- -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: ('|',
'=', ','))
- --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)
- pair-pass
- successfully paired reads with modified annotations.
- pair-fail
- raw reads that could not be assigned to a mate-pair.
- <user defined>
- annotation fields specified by the --1f or --2f
arguments.
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.