Alignment coverage information
maf_stats.py
#if $maf_source_type.maf_source == "user":
$maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
#else:
$maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
#end if
${GALAXY_DATA_INDEX_DIR}
#if $maf_source_type.maf_source == "user":
$input2.metadata.maf_index
#end if
numpy
**What it does**
This tool takes a MAF file and an interval file and relates coverage information by interval for each species.
If a column does not exist in the reference genome, it is not included in the output.
Consider the interval: "chrX 1000 1100 myInterval"
Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this:
chrX 1000 1100 myInterval H XXX YYY
chrX 1000 1100 myInterval M XXX YYY
chrX 1000 1100 myInterval R XXX YYY
where XXX and YYY are:
XXX = number of nucleotides
YYY = number of gaps
----
Alternatively, you can request only summary information for a set of intervals:
======== =========== ========
#species nucleotides coverage
======== =========== ========
hg18 30639 0.2372
rheMac2 7524 0.0582
panTro2 30390 0.2353
======== =========== ========
where **coverage** is the number of nucleotides divided by the total length of the provided intervals.