Enveomics collection

BlastTab.sumPerHit.pl

Sums the weights of all the queries hitting each subject. Often (but not necessarily) the BLAST files contain only best matches. The weights can be any number, but a common use of this Script is to add up counts (weights are integers). For example, in a BLAST of predicted genes vs some annotation source, the weights could be the number of reads recruited by each gene.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Perl.

§ Usage

BlastTab.sumPerHit.pl [opts] in_file > out_file

§ Arguments

Weights file

 -w in_file  A two-columns tab-delimited file containing the the name (column 1) and the weight (column 2) of each query.

Minimum score

 -s float 

Minimum identity (%)

 -i float 

Queries

 -m integer  Maximum number of queries. Set to 0 for all.

Normalize

 -n   Normalize weights by the number of hits per query.

Include zeroes

 -z   Add zero when weight is not found (by default: doesn't list them).

Run quietly

 -q  

blast*

 in_file  One or more BLAST files.

Output file*

 out_file  A two-columns tab-delimited file containing the summed weights per hit.

* Mandatory.