SLiMSuite REST Server

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SLiMSuite Documentation

Please note that command documentation sometimes lags behind the latest module versions. Click on module names to check current documentation.

cmd: spcode

Option Type: [?]{docs:?} X

Modules: rje_genbank rje_seqlist rje_sequence snp_mapper budapest fiesta pagsat_V1 pagsat snapper unifake

SLiMSuite species codes are designed to follow the UniprotKB organism (species) identification codes, using them wherever possible. They form part of the standard gene_SPECIES__AccNum naming convention for sequences within SLiMSuite. Species codes should be upper case, and unique for each species.

Module	Option	Description	Default
budapest	`spcode=X`	Species code for EST sequences	`None`
fiesta	`spcode=X`	Species code for EST sequences	`None`
pagsat	`spcode=X`	Species code for reference genome (if not already processed by rje_genbank)	`None`
pagsat_V1	`spcode=X`	Species code for reference genome (if not already processed by rje_genbank)	`None`
rje_genbank	`spcode=X`	Overwrite species read from file (if any!) with X	`None`
rje_seqlist	`spcode=X`	Species code for non-gnspacc format sequences	`None`
rje_sequence	`[spcode=?]{docs:?}`		`?`
snapper	`spcode=X`	Overwrite species read from file (if any!) with X if generating sequence file from genbank	`None`
snp_mapper	`spcode=X`	Overwrite species read from file (if any!) with X if generating sequence file from genbank	`None`
unifake	`spcode=X`	Species code to use if it cannot be established from sequence name	`None`