Provided by: obitools_1.2.12+dfsg-2_amd64
NAME
obiconvert - description of obiconvert obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats. Input files can be in : · fasta format · extended OBITools fasta format · Sanger fastq format · Solexa fastq format · ecoPCR format · ecoPCR database format · GenBank format · EMBL format obiconvert converts those files to the : · extended OBITools fasta format · Sanger fastq format · ecoPCR database format If no file name is specified, data is read from standard input. Examples: > obiconvert --ecopcrdb --fasta-output \ 'my_ecopcr_database' > sequences.fasta Converts an ecoPCR database in a sequence file in extended OBITools fasta format.
TAXONOMY RELATED OPTIONS
-d <FILENAME>, --database=<FILENAME> ecoPCR taxonomy Database name -t <FILENAME>, --taxonomy-dump=<FILENAME> NCBI Taxonomy dump repository name
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.
AUTHOR
The OBITools Development Team - LECA
COPYRIGHT
2019 - 2015, OBITool Development Team 1.02 12 Jan 28, 2019 OBICONVERT(1)