Exonerate

1

Hello. Is there any possibility that Exonerate, the sequence alignment tool, returns only cigar string? I mean how could we print only the string without printing unnecessary stuff like below (or without parsing output)?

**Command line: [exonerate --model affine:global --exhaustive yes tube.fasta calm.fasta --showcigar yes --showalignment no]
Hostname: [beep]**

**** (process:30145): WARNING **: 01:19:52.429: Exhaustively generating suboptimal alignments will be VERY SLOW
cigar: Query 0 100 + Target 0 100 + 266  M 13 D 3 M 13 I 2 M 5 I 1 M 66
vulgar: Query 0 100 + Target 0 100 + 266 M 13 13 G 0 3 M 13 13 G 2 0 M 5 5 G 1 0 M 66 66
-- completed exonerate analysis**


**Wanted output:** M 13 D 3 M 13 I 2 M 5 I 1 M 66


Exonerate

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Have you tried the roll your own (--ryo) output format (see the manual)? There are detailed options.

--showalignment no --showvulgar no --ryo "%Cn"

 M 5 I 2 M 3 D 2 M 10 I 1 M 15 I 1 M 10 I 1 M 18 D 1 M 16 I 3 M 7 I 1 M 15 D 2 M 5 I 1 M 10 I 1 M 38 D 4 M 47 D 1 M 2 D 1 M 7 D 2 M 22 I 2 M 4 I 2 M 18 I 2 M 2 I 1 M 24 I 1 M 4 I 1 M 21 I 2 M 11 I 1 M 25 D 1 M 9 D 1 M 12 I 1 M 20


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