addLoci

Description:  Adds locus lines to an SQT file based on matches to the given database. This can be used to add protein locus IDs to files not containing them (e.g. from BiblioSpec output) or to replace the locus IDs in an SQT with ones from a different database.

Usage:  addLoci.pl [options]  <fasta file> <sqt file> [<sqt file>...]

Input: <fasta file> - a fasta file containing the proteins to search for peptide matches. <sqt file> - an output file from a search algorithm (SEQUEST or BiblioSpec) to which locus lines will be added. Any number of sqt files can be listed. Note: it is much faster to run several sqt files together than it is to run each separately.

Output:   - a new SQT file is printed to stdout OR with the -overwrite option, the input files will be changed in place. The changes include three additional lines in the header including the database used. Also added are locus lines after every matching peptide for which a protein was found.

Options:

• -replace - delete any existing locus lines and print only those loci found in the given database. Default is to add the new locus lines to those already in the file.
• -overwrite - change the input SQT files inplace. This option is recommended when using multiple SQT files
• -verbosity <0|1|2> - set the level of output to stderr. Level 0 is silent. Default is 1.

Bugs:

• If a peptide occurs more than once in a protein, the locus will be listed multiple times.
• When loci are added to the exisiting ones, no check is made to see if the new locus was already found. It will be added again.