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. ----- .. class:: warningmark **Note** Any block/s not containing exactly 2 species will be omitted. ----- **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