PeptideMapperCLI - PeptideMapper Command Line Interface

PeptideMapper can be used to map sequences and sequence tags to a database of protein sequences. This wiki page describes its command line usage.

Command Line

PeptideMapper is distributed in the compomics-utilities package. PeptideMapperCLI can be run from the utilities jar file as detailed below.

java -cp utilities-X.Y.Z.jar com.compomics.util.experiment.identification.protein_inference.executable.PeptideMapping -[p|t] <InputFasta> <InputList> <OutputResultList> [<UtilitiesParameterFile>]

Please replace X.Y.Z by the version used, e.g. 4.7.2.


Option Value Description
p|t p or t Type of mapping, p for peptide sequences, t for sequence tags. (Mandatory)
InputFasta Path to File Path to a FASTA file containing the protein sequences. (Mandatory)
InputList Path to File Path to a file containing the input sequences or tags.
OutputResultList Path to File Path to a file where to store the result of the mapping.
UtilitiesParameterFile Path to File Path to a file containing the identification parameters.

Supported Formats

Protein Sequence database

PeptideMapper supports protein sequence databases in the FASTA format. In a FASTA file each sequence is represented by a header and the sequence itself. The header contains information about the protein, e.g., protein accession number, database and species. However, the format of the header varies from database to database. PeptideMapper supports the most encountered databases like UniProt, Ensembl, NextProt, NCBI and IPI, plus a long list of other databases. For home made databases we recommend our generic FASTA format.

Peptide Sequences

Peptide sequences should be provided in a text file, one sequence per line.


Sequence Tags

Sequence tags should be provided in a text file, one tag per line, with the tag components separated by a comma.


Parameters File

The parameters file should be in the json format. Parameters files can be generated using the IdentificationParametersCLI.


Example to map a peptide list to a FASTA file:

java -cp utilities-X.Y.Z.jar com.compomics.util.experiment.identification.protein_inference.executable.PeptideMapping -p exampleFiles/PeptideMapping/yeast.fasta exampleFiles/PeptideMapping/yeast-pep-1k.csv result-file.csv