obiextract1

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.

Options

-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.

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)

Options

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

--DEBUG: Sets logging in debug mode.

Obiextract modified sequence attributes

•: count

Obiextract used sequence attribute

•: count