Assigns a class to alignments made with the blat alignment tool (http://www.kentinformatics.com/).
For example it converts the following lines of blat output for a given sequence:
8712 33 0 0 2 13 1 6 + TraesCS1A02G428900.genomic 8758 0 8758 Chr1A 598636984 586868637 586877388 3 4528,2715,1502, 0,4540,7256, 586868637,586873171,586875886,
7460 76 0 0 8 75 9 178 + TraesCS1A02G428900.genomic 8758 371 7982 Chr1A 598636984 501546808 501554522 14 338,3430,264,52,127,568,22,238,243,163,750,616,447,278, 371,730,4163,4450,4514,4641,5209,5231,5471,5714,5877,6639,7256,7704, 501546808,501547146,501550577,501550891,501550943,501551157,501551730,501551754,501551993,501552237,501552429,501553179,501553795,501554244,
7443 67 0 0 8 105 6 91 + TraesCS1A02G428900.genomic 8758 370 7985 Chr1A 598636984 522990743 522998344 13 339,1544,2131,52,22,99,562,22,238,406,750,985,360, 370,751,2296,4450,4514,4548,4647,5209,5231,5471,5877,6639,7625, 522990743,522991082,522992626,522994807,522994859,522994881,522994983,522995550,522995574,522995813,522996249,522996999,522997984,
308 2 0 0 1 3 0 0 - TraesCS1A02G428900.genomic 8758 7682 7995 Chr1A 598636984 586869002 586869312 2 6,304, 763,772, 586869002,586869008,
302 2 0 0 0 0 0 0 - TraesCS1A02G428900.genomic 8758 7682 7986 Chr1A 598636984 522990744 522991048 1 304, 772, 522990744,
301 3 0 0 0 0 0 0 - TraesCS1A02G428900.genomic 8758 7682 7986 Chr1A 598636984 501546808 501547112 1 304, 772, 501546808,
283 10 0 0 2 12 1 14 - TraesCS1A02G428900.genomic 8758 7680 7985 Chr1A 598636984 320954149 320954456 3 232,43,18, 773,1016,1060, 320954149,320954395,320954438,
308 2 0 0 0 0 1 3 - TraesCS1A02G428900.genomic 8758 365 675 Chr1A 598636984 586876312 586876625 2 304,6, 8083,8387, 586876312,586876619,
301 2 0 0 0 0 0 0 - TraesCS1A02G428900.genomic 8758 372 675 Chr1A 598636984 522998041 522998344 1 303, 8083, 522998041,
294 5 0 0 1 1 1 2 - TraesCS1A02G428900.genomic 8758 375 675 Chr1A 598636984 501554221 501554522 2 21,278, 8083,8105, 501554221,501554244,
To:
TraesCS1A02G428900.genomic full-length with tGaps with qGaps with mismatches
Where the alignment class reported is the "best". Applied to a full alignment we can summarise the cases:
> python ~/dev/creamcar/creamcar.py IWGSC_v1.1_to_v2.0.genomic.notPerfectMatch.1A.psl|cut -d ' ' -f2-|sort|uniq -c|sort -k1,1nr
203 full-length with tGaps with qGaps with mismatches
147 full-length with tGaps with qGaps
123 full-length with Ns
114 full-length with mismatches
37 full-length with qGaps
36 full-length with qGaps with mismatches
24 full-length with tGaps with mismatches
15 not full-length with tGaps with qGaps with mismatches
13 not full-length
7 not full-length with mismatches
5 full-length with tGaps
4 full-length with Ns with mismatches
4 full-length with tGaps with qGaps with Ns with mismatches
3 not full-length with qGaps with mismatches
2 full-length with tGaps with qGaps with Ns
2 not full-length with tGaps with qGaps
1 full-length with qGaps with Ns with mismatches
1 not full-length with qGaps
1 not full-length with tGaps with mismatches