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OBISUBSET(1) OBITools OBISUBSET(1)

NAME

obisubset - description of obisubset

The obisubset command extracts a subset of samples from a sequence file after its dereplication using obiuniq program.

OBISUBSET SPECIFIC OPTIONS

-s <TAGNAME>, --sample=<TAGNAME>,
The option -s allows to specify the tag containing sample descriptions, the default value is set to merged_sample.

Example:

> obiuniq -m sample seq1.fasta > seq2.fasta
> obisubset -s merged_sample -n sample1 seq2.fasta > seq3.fasta


After the dereplication of the sequences using the in the new attribute merged_sample.




-o <TAGNAME>, --other-tag=<TAGNAME>,
Another tag to clean according to the sample subset

Example:

> obisubset -s merged_sample -o -n sample1 seq2.fasta > seq3.fasta





-l <FILENAME>, --sample-list=<FILENAME>,
File containing the samples names (one sample id per line).

Example:

> obisubset -s merged_sample -o -l ids.txt seq2.fasta > seq3.fasta





-p <REGEX>, --sample-pattern=<REGEX>,
A regular expression pattern matching the sample ids to extract.

Example:

> obisubset -s merged_sample -o -p "negative_.*" seq2.fasta > seq3.fasta





-n <SAMPLEIDS>, --sample-name=<SAMPLEIDS>,
A sample id to extract

Example:

> obisubset -s merged_sample -o -n sample1 seq2.fasta > seq3.fasta





OPTIONS TO SPECIFY INPUT FORMAT

Restrict the analysis to a sub-part of the input file

--skip <N>
The N first sequence records of the file are discarded from the analysis and not reported to the output file

--only <N>
Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the –skip option.

Sequence annotated format

--genbank
Input file is in genbank format.

--embl
Input file is in embl format.

--fasta
Input file is in fasta format (including OBITools fasta extensions).

--sanger
Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers).

--solexa
Input file is in fastq format produced by Solexa (Ga IIx) sequencers.

--ecopcr
Input file is in ecoPCR format.

--ecopcrdb
Input is an ecoPCR database.

Specifying the sequence type

--nuc
Input file contains nucleic sequences.

--prot
Input file contains protein sequences.

OPTIONS TO SPECIFY OUTPUT FORMAT

Standard output format

--fasta-output
Output sequences in OBITools fasta format

--fastq-output
Output sequences in Sanger fastq format

Generating an ecoPCR database

--ecopcrdb-output=<PREFIX_FILENAME>
Creates an ecoPCR database from sequence records results

Miscellaneous option

--uppercase
Print sequences in upper case (default is lower case)

COMMON OPTIONS

-h, --help
Shows this help message and exits.

--DEBUG
Sets logging in debug mode.

OBISUBSET MODIFIES SEQUENCE ATTRIBUTES

•
count

•
merged_*





OBISUBSET USED SEQUENCE ATTRIBUTE

  • count
  • merged_*



AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team
January 28, 2019 1.02 12