NAME

CollapseSeq.py - emoves duplicate sequences from FASTA/FASTQ files

DESCRIPTION

usage: CollapseSeq.py [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-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 | --minf MIN_FIELD]
Removes duplicate sequences from FASTA/FASTQ files

help:

--version
show program's version number and exit
-h, --help
show this help message and exit

standard arguments:

-s SEQ_FILES [SEQ_FILES ...]
A list of FASTA/FASTQ files containing sequences to process. (default: None)
-o OUT_FILES [OUT_FILES ...]
Explicit output file name(s). Note, this argument cannot be used with the --failed, --outdir, or --outname arguments. If unspecified, then the output filename will be based on the input filename(s). (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)
--log LOG_FILE
Specify to write verbose logging to a file. 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: ('|', '=', ','))

collapse arguments:

-n 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)
--uf UNIQ_FIELDS [UNIQ_FIELDS ...]
Specifies a set of annotation fields that must match for sequences to be considered duplicates. (default: None)
--cf COPY_FIELDS [COPY_FIELDS ...]
Specifies a set of annotation fields to copy into the unique sequence output. (default: None)
--act {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)
--inner
If specified, exclude consecutive missing characters at either end of the sequence. (default: False)
--keepmiss
If specified, sequences with more missing characters than the threshold set by the -n 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)
--maxf MAX_FIELD
Specify the field whose maximum value determines the retained sequence; mutually exclusive with --minf. (default: None)
--minf MIN_FIELD
Specify the field whose minimum value determines the retained sequence; mutually exclusive with --minf. (default: None)

output files:

collapse-unique
unique sequences. Contains one representative from each set of duplicate sequences. The retained representative is determined by user defined criteria.
collapse-duplicate
raw reads which are duplicates of the sequences retained in the collapse-unique file.
collapse-undetermined
raw reads which were excluded from consideration due to having too many N characters in the sequence.

output annotation fields:

DUPCOUNT
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.
<user defined>
annotation fields specified by the --cf parameter.

AUTHOR


This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.