obiextract - description of obiextract
The obiextract command extract a subset of samples from a
complete dataset.
Extracted sample names can be specified or by indicating their
names using option on the command line or by indicating a file name
containing a sample name per line
The count attribute of the sequence and the slot describing
distribution of the sample occurrences among samples are modified according
to the selected samples.
A sequence not present in at least one of the selected samples is
not conserved in the output of obiextract.
- -s <KEY>,
--sample=<KEY>
- Attribute containing sample descriptions. By default the attribute name
used for describing samples is set to merged_sample.
- -e <SAMPLE_NAME>,
--extract=<KEY>
Attribute indicating which <SAMPLE_NAME> have to be
extracted. Several
-p options can be added for specifying several
samples. If you want to extract a large number of samples, please refer to the
-E option described below
TIP:
The <KEY> can be simply the key of an
attribute, or a Python expression similarly to the -p option of
obigrep.
Example:
> obiextract -e sampleA -e sampleB allseqs.fasta > samplesAB.fasta
This command extracts from the allseqs.fasta file data
related to samples A and B.
- -E <FILENAME>,
--extract-list=<FILENAME>
Allows for indicating a file name where a list of sample
is stored. The file must be a simple text file with a sample name per
line.
Example:
> obiextract -E subset.txt allseqs.fasta > subset_samples.fasta
This command extracts from the allseqs.fasta file data
related to samples listed in the subset.txt 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.
- --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.
- --nuc
- Input file contains nucleic sequences.
- --prot
- Input file contains protein sequences.
- --fasta-output
- Output sequences in OBITools fasta format
- --ecopcrdb-output=<PREFIX_FILENAME>
- Creates an ecoPCR database from sequence records results
- --uppercase
- Print sequences in upper case (default is lower case)
- --DEBUG
- Sets logging in debug mode.
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