proteins_to_sequences allows the user to look up the amino acid sequences corresponding to each of a set of proteins (represented as MD5 hash values) This command allows you to get back formatted fasta files.
Example:
proteins_to_sequences [arguments] < input > output
The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the identifer. If another column contains the identifier use
-c N
where N is the column (from 1) that contains the subsystem.
This is a pipe command. The input is taken from the standard input, and the output is to the standard output.
This is used only if the column containing the subsystem is not the last column.
This is used to request a fasta output file (dropping all of the other columns in the input lines). It defaults to outputing just a fasta entry.
This is used to ask for "fasta comments" formed from one or more columns (comma-separated)
The standard output is jsut a fasta file with the sequence. You can also get a tab-delimited file by using -fasta=0. The tab-delimited format consists of the input file with an extra column of sequence added.
Input lines that cannot be extended are written to stderr.
To install Bio::KBase, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::KBase
CPAN shell
perl -MCPAN -e shell install Bio::KBase
For more information on module installation, please visit the detailed CPAN module installation guide.