.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH PAIRSEQ.PY "1" "May 2020" "PairSeq.py 0.6.0" "User Commands"
.SH NAME
PairSeq.py \- Sorts and matches sequence records with matching coordinates across files
.SH DESCRIPTION
usage: PairSeq.py [\-\-version] [\-h] \fB\-1\fR SEQ_FILES_1 [SEQ_FILES_1 ...] \fB\-2\fR
.IP
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}]
.PP
Sorts and matches sequence records with matching coordinates across files
.SS "help:"
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "standard arguments:"
.TP
\fB\-1\fR SEQ_FILES_1 [SEQ_FILES_1 ...]
An ordered list of FASTA/FASTQ files containing
head/primary sequences. (default: None)
.TP
\fB\-2\fR SEQ_FILES_2 [SEQ_FILES_2 ...]
An ordered list of FASTA/FASTQ files containing
tail/secondary sequences. (default: None)
.TP
\fB\-\-outdir\fR 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)
.TP
\fB\-\-outname\fR 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)
.TP
\fB\-\-failed\fR
If specified create files containing records that fail
processing. (default: False)
.TP
\fB\-\-fasta\fR
Specify to force output as FASTA rather than FASTQ.
(default: None)
.TP
\fB\-\-delim\fR DELIMITER DELIMITER DELIMITER
A list of the three delimiters that separate
annotation blocks, field names and values, and values
within a field, respectively. (default: ('|', '=',
\&','))
.SS "pairing arguments:"
.TP
\fB\-\-1f\fR 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)
.TP
\fB\-\-2f\fR 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)
.TP
\fB\-\-act\fR {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)
.TP
\fB\-\-coord\fR {illumina,solexa,sra,454,presto}
The format of the sequence identifier which defines
shared coordinate information across mate pairs.
(default: presto)
.SS "output files:"
.IP
pair\-pass
.IP
successfully paired reads with modified annotations.
.IP
pair\-fail
.IP
raw reads that could not be assigned to a mate\-pair.
.SS "output annotation fields:"
.IP
<user defined>
.IP
annotation fields specified by the \fB\-\-1f\fR or \fB\-\-2f\fR arguments.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.