db_prep

Command line tool that separates coarse-grained peptide sequence clusters of the specified range of peptide sequence lengths from a peptide sequence database (FASTA format). The output .pep files are directly used by the HiCOPS for database constructions and processing.

General Syntax

$ $HICOPS_INSTALL/tools/dbtools/db_prep [peptide_seqs.fasta] [min_len] [max_len] [Optional: output_path]

Paramaters:

• peptide_seqs: path to peptide sequence database.
• min_len: minimum length peptide sequences to extract.
• max_len: maximum length peptide sequences to extract.
• output_path: path where the .pep files will be written.

Example Usage

$ $HICOPS_INSTALL/tools/dbtools/db_prep ./human_peptides.fasta 6 20 ./output
Processing peptides of length: 6
Processing peptides of length: 7
Processing peptides of length: 8
Processing peptides of length: 9
Processing peptides of length: 10
Processing peptides of length: 11
Processing peptides of length: 12
Processing peptides of length: 13
Processing peptides of length: 14
Processing peptides of length: 15
Processing peptides of length: 16
Processing peptides of length: 17
Processing peptides of length: 18
Processing peptides of length: 19
Processing peptides of length: 20

$ ls output
10.peps  11.peps  12.peps  13.peps  14.peps  15.peps  16.peps  17.peps  18.peps  19.peps  20.peps  6.peps  7.peps  8.peps  9.peps