chen2meme

Usage:

chen2meme [options]

Description

Read a CHEN matrix file and convert to MEME format. You may concatenate files for more than one motif.

Input

Reads concatenated CHEN files from standard input.

Concatenated CHEN files describe one or more motifs. Each motif has a header line and a position-weight matrix.

Sample Input
>NANOG
2       64      4       10
1       66      1       12
52      1       0       27
0       0       0       80
0       0       0       80
0       5       74      1
3       1       1       75
3       49      14      14
57      9       0       14
1       0       3       76
1       3       46      30
4       48      12      16
30      16      3       31
31      12      19      18
41      12      12      15
16      20      12      32
>OCT4
11      216     13      99
168     10      1       160
1       6       2       330
12      0       8       319
21      92      213     13
98      5       5       231
68      93      37      141
326     0       4       9
0       0       0       339
0       0       319     20
4       289     19      27
288     1       1       49
212     25      73      29
294     8       23      14
55      28      54      202
      

Output

Options

Option Parameter Description Default Behavior
General Options