.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH COLLAPSESEQ.PY "1" "May 2020" "CollapseSeq.py 0.6.0" "User Commands"
.SH NAME
CollapseSeq.py \- emoves duplicate sequences from FASTA/FASTQ files
.SH DESCRIPTION
usage: CollapseSeq.py [\-\-version] [\-h] \fB\-s\fR SEQ_FILES [SEQ_FILES ...]
.TP
[\-o OUT_FILES [OUT_FILES ...]] [\-\-outdir OUT_DIR]
[\-\-outname OUT_NAME] [\-\-log LOG_FILE] [\-\-failed]
[\-\-fasta] [\-\-delim DELIMITER DELIMITER DELIMITER]
[\-n MAX_MISSING] [\-\-uf UNIQ_FIELDS [UNIQ_FIELDS ...]]
[\-\-cf COPY_FIELDS [COPY_FIELDS ...]]
[\-\-act {min,max,sum,set} [{min,max,sum,set} ...]]
[\-\-inner] [\-\-keepmiss]
[\-\-maxf MAX_FIELD | \fB\-\-minf\fR MIN_FIELD]
.PP
Removes duplicate sequences from FASTA/FASTQ 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\-s\fR SEQ_FILES [SEQ_FILES ...]
A list of FASTA/FASTQ files containing sequences to
process. (default: None)
.TP
\fB\-o\fR OUT_FILES [OUT_FILES ...]
Explicit output file name(s). Note, this argument
cannot be used with the \fB\-\-failed\fR, \fB\-\-outdir\fR, or
\fB\-\-outname\fR arguments. If unspecified, then the output
filename will be based on the input filename(s).
(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\-\-log\fR LOG_FILE
Specify to write verbose logging to a file. 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 "collapse arguments:"
.TP
\fB\-n\fR MAX_MISSING
Maximum number of missing nucleotides to consider for
collapsing sequences. A sequence will be considered
undetermined if it contains too many missing
nucleotides. (default: 0)
.TP
\fB\-\-uf\fR UNIQ_FIELDS [UNIQ_FIELDS ...]
Specifies a set of annotation fields that must match
for sequences to be considered duplicates. (default:
None)
.TP
\fB\-\-cf\fR COPY_FIELDS [COPY_FIELDS ...]
Specifies a set of annotation fields to copy into the
unique sequence output. (default: None)
.TP
\fB\-\-act\fR {min,max,sum,set} [{min,max,sum,set} ...]
List of actions to take for each copy field which
defines how each annotation will be combined 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.
(default: None)
.TP
\fB\-\-inner\fR
If specified, exclude consecutive missing characters
at either end of the sequence. (default: False)
.TP
\fB\-\-keepmiss\fR
If specified, sequences with more missing characters
than the threshold set by the \fB\-n\fR parameter will be
written to the unique sequence output file with a
DUPCOUNT=1 annotation. If not specified, such
sequences will be written to a separate file.
(default: False)
.TP
\fB\-\-maxf\fR MAX_FIELD
Specify the field whose maximum value determines the
retained sequence; mutually exclusive with \fB\-\-minf\fR.
(default: None)
.TP
\fB\-\-minf\fR MIN_FIELD
Specify the field whose minimum value determines the
retained sequence; mutually exclusive with \fB\-\-minf\fR.
(default: None)
.SS "output files:"
.IP
collapse\-unique
.IP
unique sequences. Contains one representative from each set of
duplicate sequences. The retained representative is determined by
user defined criteria.
.IP
collapse\-duplicate
.IP
raw reads which are duplicates of the sequences retained in the
collapse\-unique file.
.IP
collapse\-undetermined
.IP
raw reads which were excluded from consideration due to having too
many N characters in the sequence.
.SS "output annotation fields:"
.IP
DUPCOUNT
.IP
total number of sequences within the set of duplicates for each
retained unique sequence. Meaning, the copy number of each unique
sequence within the data file.
.IP
<user defined>
.IP
annotation fields specified by the \fB\-\-cf\fR parameter.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.