PeptideMapperCLI

PeptideMapperCLI - PeptideMapper Command Line Interface

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

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General Command Line

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

Command Line Options

Option	Value	Description
p	t	p
InputFasta	Path to File	Path to a fasta file containing the protein sequences
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.

QAERYDDMASAMK
NEPLSNEER
ANQIEYYFVS
...

Sequence Tags

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

211.521,LLQ,358.521
421.115,GAEM,97.555
85.455,YS,854.265
502.596,SGLTR,142.503
...

Parameters File

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

## Examples ##

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