obiconvert1
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 : obiconvert converts those files to the : if no file name is specified, data is read from standard input. examples:
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
OBIToolsfasta 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.