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Command-Line Interface

In addition to the MatchMiner web interface provided on this site, a command-line interface is also available. This interface may be useful if you want to integrate MatchMiner processesing as part of a chain using pipes and filters. This page describes the options that can be specified when using the command-line interface.

System Requirements

To get started, first, download the command-line jar file.

Command-line syntax

The general form of the interface is:

java -jar matchminer.jar [Optional JVM parameters] [MatchMiner parameters (see below)]

An example of a lookup operation

java -jar matchminer.jar -Tlookup -ORhuman -I1symbol -IA1officialname -IF1c:\documents\geneNames.txt -OTaccno -Arefseqnumber -OFc:\documents\output.txt -HStrue

An example of a merge operation

java -jar matchminer.jar -Tmerge -ORmouse -I1accno -IA1refseqaccnumber -IF1c:\documents\accessions.txt -I2clone -IA2clone -IF2c:\documents\clones.txt -HSfalse

The table below describes the command-line parameters for using MatchMiner. If any option is not specified, but is required to complete the operation, then the user will be prompted to provide the missing information.

Option Prefix Possible Values Operation Used

Operation

-Tvalue

lookup, merge

Both

Organism

-ORvalue

human, mouse

Both

Input type for the first file

-I1value

The following are the available input types, followed in brackets by the full name of the choice and the organisms for which the algorithm is appropriate. What you choose for Input type for the first file must be consistent with your selection for Input algorithm for the first file.

  • band [Cytogenetic Location - human]
  • clone [Clone - human, mouse]
  • accno [GenBank Accession Number - human, mouse]
  • symbol [Symbol - human, mouse]
  • name [Name - human, mouse]
  • affy [Affymetrix Id - human, mouse]
  • unigene [UniGene Cluster Id - human, mouse]
  • entrezgene [Entrez Gene Id - human, mouse]

Both

Input type for the second file

-I2value

The following are the available input types, followed in brackets by the full name of the choice and the organisms for which the algorithm is appropriate. What you choose for Input type for the second file must be consistent with your selection for Input algorithm for the second file.

  • band [Cytogenetic Location - human]
  • clone [Clone - human, mouse]
  • accno [GenBank Accession Number - human, mouse]
  • symbol [Symbol - human, mouse]
  • name [Name - human, mouse]
  • affy [Affymetrix Id - human, mouse]
  • unigene [UniGene Cluster Id - human, mouse]
  • entrezgene [Entrez Gene Id - human, mouse]

Merge

Input algorithm for the first file

-IA1value

The following are the available algorithm options, followed in brackets by the full name of the choice and the input type for which the algorithm is appropriate. What you choose for Input algorithm for the first file must be consistent with your selection for Input type for the first file.

  • band [All - band]
  • clone [cDNA (IMAGE) - clone]
  • nonimageclone [cDNA (Non-IMAGE) - clone]
  • combclone [cDNA (IMAGE and non-IMAGE) - clone]
  • fishclone [FISH-mapped BAC - clone]
  • genebankaccnumber [GenBank(All inc. RefSeq) - accno]
  • refseqaccnumber [RefSeq (DNA, RNA, and Protein) - accno]
  • dnaaccnumber [DNA Acc Num (inc. RefSeq) - accno]
  • refseqdnaaccnumber [RefSeq (DNA) - accno]
  • rnaaccnumber [RNA Acc Num (inc. RefSeq) - accno]
  • refseqrnaaccnumber [RefSeq (RNA) - accno]
  • proteinaccnumber [Protein Acc Num (inc. RefSeq) - accno]
  • refseqproteinaccnumber [RefSeq (Protein) - accno]
  • estaccnumber [EST Acc Number - accno]
  • name [Official then Alias if Official not available - symbol]
  • officialname [Official - symbol]
  • allnames [All(Official and Alias) - symbol]
  • longname [Long Name - name]
  • unigenenumber [All - unigene]
  • affy [All - affy]
  • entrezgeneid [All - entrezgene]

Both

Input algorithm for the second file

-IA2value

The following are the available algorithm options, followed in brackets by the full name of the choice and the input type for which the algorithm is appropriate. What you choose for Input algorithm for the second file must be consistent with your selection for Input type for the second file.

  • band [All - band]
  • clone [cDNA (IMAGE) - clone]
  • nonimageclone [cDNA (Non-IMAGE) - clone]
  • combclone [cDNA (IMAGE and non-IMAGE) - clone]
  • fishclone [FISH-mapped BAC - clone]
  • genebankaccnumber [GenBank(All inc. RefSeq) - accno]
  • refseqaccnumber [RefSeq (DNA, RNA, and Protein) - accno]
  • dnaaccnumber [DNA Acc Num (inc. RefSeq) - accno]
  • refseqdnaaccnumber [RefSeq (DNA) - accno]
  • rnaaccnumber [RNA Acc Num (inc. RefSeq) - accno]
  • refseqrnaaccnumber [RefSeq (RNA) - accno]
  • proteinaccnumber [Protein Acc Num (inc. RefSeq) - accno]
  • refseqproteinaccnumber [RefSeq (Protein) - accno]
  • estaccnumber [EST Acc Number - accno]
  • name [Official then Alias if Official not available - symbol]
  • officialname [Official - symbol]
  • allnames [All(Official and Alias) - symbol]
  • longname [Long Name - name]
  • unigenenumber [All - unigene]
  • affy [All - affy]
  • entrezgeneid [All - entrezgene]

Merge

First input file

-IF1value

Relative Path of the file

Both

Second input file

-IF2value

Relative Path of the file

Merge

Output identifier type

-OTvalue

The following are the available input types, followed in brackets by the full name of the choice and the organisms for which the algorithm is appropriate. What you choose for Output identifier type must be consistent with your selection for Output algorithm.

  • band [Cytogenetic Location - human]
  • chrloc [Sequence Location Number(BP) - human]
  • clone [Clone - human, mouse]
  • accno [GenBank Accession Number - human, mouse]
  • symbol [Symbol - human, mouse]
  • name [Name - human, mouse]
  • affy [Affymetrix Id - human, mouse]
  • unigene [UniGene Cluster Id - human, mouse]
  • entrezgene [Entrez Gene Id - human, mouse]

Lookup

Output algorithm

-Avalue

The following are the available algorithm options, followed in brackets by the full name of the choice and the input type for which the algorithm is appropriate. What you choose for Input algorithm for the first file must be consistent with your selection for Input type for the first file.

  • band [ALL - band]
  • ucscband [UCSC - band]
  • clone [cDNA (IMAGE and non-IMAGE) - clone]
  • fishclone [FISH-mapped BAC - clone]
  • officialname [Official - symbol]
  • name [Official then Alias if Official not available - symbol]
  • allnames [All(Official and Alias) - symbol]
  • longname [Long Name - name]
  • unigenenumber [Active UniGene Cluster Ids - unigene]
  • transcriptionstart [Transcription Start - chrloc]
  • transcriptionend [Transcription End - chrloc]
  • transcriptionsbothends [Transcription Start and End - chrloc]
  • refseqnumber [RefSeq (DNA, RNA and Protein) - accno]
  • genebankaccnumber [GenBank (inc. RefSeq) - accno]
  • dnaaccnumber [DNA Acc Num (inc. RefSeq) - accno]
  • rnaaccnumber [RNA Acc Num (inc. RefSeq) - accno]
  • proteinaccnumber [Protein Acc Num (inc. RefSeq) - accno]
  • estaccnumber [EST Acc Num - accno]
  • affy [All - affy]
  • entrezgeneid [All - entrezgene]

Lookup

Output File

-OFvalue

Relative Path of the file or stdout

Both

Output File Format

-FFvalue

The following are the available File format options, followed in brackets by the full description of the choice.

  • text [Text]
  • gominer [GoMiner Format]
Lookup

Want to hide data source details?

-HSvalue

true, false

Both

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MatchMiner is a development of the Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology (LMP), Center for Cancer Research (CCR) National Cancer Institute (NCI).

If you have any problems, questions or feedback on the tool, please email us.

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