from pairwise alignments
getIndels.py $input1 $out_file1
numpy
.. class:: infomark
**What it does**
This tool estimates the number of indels for every alignment block of the MAF file.
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.. class:: warningmark
**Note**
Any block/s not containing exactly 2 species will be omitted.
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**Example**
- For the following alignment block::
a score=7233.0
s hg18.chr1 100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT
s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC----
- running this tool will return::
#Block Source Seq1_Start Seq1_End Seq2_Start Seq2_End Indel_length
1 hg18.chr1 101 102 202 204 2
1 rheMac2.chr11 103 104 204 205 1
1 rheMac2.chr11 129 133 229 230 4