fids_to_protein_sequences

fids_to_protein_sequences allows the user to look up the amino acid sequences corresponding to each of a set of fids. You can also get the sequence from proteins (i.e., md5 values). This routine saves you having to look up the md5 sequence and then accessing the protein string in a separate call.

Example:

    fids_to_protein_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.

Documentation for underlying call

This script is a wrapper for the CDMI-API call fids_to_protein_sequences. It is documented as follows:

  $return = $obj->fids_to_protein_sequences($fids)

Parameter and return types

$fids is a fids
$return is a reference to a hash where the key is a fid and the value is a protein_sequence
fids is a reference to a list where each element is a fid
fid is a string
protein_sequence is a string

Command-Line Options

-c Column

This is used only if the column containing the subsystem is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

-fasta

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.

-fc Columns [ construct comment for fasta from these columns ]

This is used to ask for "fasta comments" formed from one or more columns (comma-separated)

Output Format

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.