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.cli.peptide_mapper.PeptideMapperCLI -[p|t] <InputFasta> <InputList> <OutputResultList> [<UtilitiesParameterFile>]
Please replace X.Y.Z by the version used, e.g. 5.0.39.
Options
| 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.
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.
Example
Example to map a peptide list to a FASTA file:
java -cp utilities-X.Y.Z.jar com.compomics.cli.peptide_mapper.PeptideMapperCLI -p exampleFiles/PeptideMapping/yeast.fasta exampleFiles/PeptideMapping/yeast-pep-1k.csv result-file.csv