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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 related format¶
- --fasta
- Input file is in fasta format (including OBITools fasta extensions).
fastq related format¶
- --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 related format¶
- --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
| July 27, 2019 | 1.02 13 |