Revamped Biopiece: analyze_vals

[Martin Asser Hansen]

Hello all,

I have rewritten analyze_vals so it now works in a more logical way and interfaces nicely with write_tab in pretty print mode.

Here is an example:

read_fastq -i test.fq | trim_seq | analyze_vals | write_tab -cpx

+----------+------------+-------+-----+-----+-----+------+

| KEY      | TYPE       | COUNT | MIN | MAX | SUM | MEAN |

+----------+------------+-------+-----+-----+-----+------+

| SEQ_NAME | Alphabetic |     3 |  42 |  42 | 126 | 42.0 |

| SEQ      | Alphabetic |     3 |  77 | 118 | 272 | 90.7 |

| SEQ_LEN  | Numeric    |     3 |  77 | 118 | 272 | 90.7 |

| SCORES   | Alphabetic |     3 |  77 | 118 | 272 | 90.7 |

+----------+------------+-------+-----+-----+-----+------+

More info here:

https://code.google.com/p/biopieces/wiki/analyze_vals

bp_update && bp_test

Cheers,

Martin

[Asker Brejnrod]

Hvordan går det ned med SCORES værdier, de ser ikke ud som om de er numeriske? Kan man regne gennemsnit og den slags med analyze_vals?

Asker

2013/10/15 Martin Asser Hansen <martin...@gmail.com>

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[Martin Asser Hansen]

I have written a separate Biopieces analyze_scores for fine grained analysis of Illumina type quality scores. See the announcement post.

Cheers,

Martin 

[Martin Asser Hansen]

Hello all,

I realized that the original logic in analyze_vals where you could choose to output the results to a file and also control if the stream should terminate was rather important. So I have reintroduced the -o and -x switches:

https://code.google.com/p/biopieces/wiki/analyze_vals

bp_update && bp_test

Cheers,

Martin