taipale2meme - MEME Suite

# The MEME Suite

## Motif-based sequence analysis tools

## taipale2meme

### Usage:

`taipale2meme [options]`

### Description

Convert a file containing the tab separated columns exported from the spreadsheet of Taipale results into MEME motif format.

### Input

Reads a Taipale file from standard input.

A Taipale file describes one or more motifs in terms of a probability matrix in column orientation.

The Taipale file must be exported from the Excel spreadsheet using the following steps:

1. Open the xls file in OpenOffice (presumably Excel will work the same)
2. Select "Save As" from the File menu
3. Change the file name to "sheetX" where X is the number of the sheet, set the output type as "Text CSV (.csv)", press save
4. Leave the character set as UTF-8, change the field delimiter to {Tab} and leave the text delimitter as "
5. You should now have a file called sheetX.csv
6. Close OpenOffice
7. Repeat from step 1 as needed for other sheets

See the example Taipale file.

### Output

### Options

Option | Parameter | Description | Default Behavior
--- | --- | --- | ---
General Options
-nc | column | Repeat this option to specify which file columns should be used to create the motif names by joining with "_". | The first non-empty column is used as the motif name
-oc | column | Repeat this option to specify one or more columns that should be empty in the line of information that identifies the motif. If the column is not empty then the motif is skipped. | All motifs are kept.
-postfix | appended text | Specify text to append to the motif names. | Motif names are left unchanged.
-strands | 1|2 | Specify if the PWM was generated from single or double stranded datasets. | Assumes the PWM was generated from a double stranded dataset.

### Example Taipale file

    "TABLE S1"
    "MEASURED BINDING PROFILES (DATA FOR FIG1D)"
    "GLI1"	1	2	3	4	5	6	7	8	9	10	14
    "A"	0.010	0.855	0.021	0.000	0.855	0.000	0.124	0.040	0.982	0.287	0.033
    "C"	0.001	0.069	0.972	1.000	0.069	1.000	0.876	0.914	0.006	0.518	0.068
    "G"	0.973	0.076	0.000	0.000	0.015	0.000	0.000	0.008	0.004	0.097	0.792
    "T"	0.016	0.000	0.006	0.000	0.061	0.000	0.000	0.038	0.008	0.098	0.107

    "GLI2"	1	2	3	4	5	6	7	8	9	10	14
    "A"	0.000	0.822	0.041	0.000	0.839	0.000	0.098	0.013	0.997	0.383	0.040
    "C"	0.000	0.090	0.959	1.000	0.064	1.000	0.902	0.887	0.000	0.361	0.156
    "G"	0.981	0.088	0.000	0.000	0.010	0.000	0.000	0.005	0.000	0.121	0.713
    "T"	0.018	0.000	0.000	0.000	0.087	0.000	0.000	0.095	0.003	0.135	0.091

    "GLI3"	1	2	3	4	5	6	7	8	9	10	14
    "A"	0.004	0.785	0.034	0.000	0.767	0.000	0.147	0.054	0.937	0.307	0.052
    "C"	0.000	0.097	0.966	1.000	0.106	1.000	0.853	0.846	0.031	0.359	0.133
    "G"	0.969	0.119	0.000	0.000	0.024	0.000	0.000	0.013	0.004	0.181	0.652
    "T"	0.027	0.000	0.000	0.000	0.104	0.000	0.000	0.088	0.027	0.154	0.163

    "Ci"	1	2	3	4	5	6	7	8	9	10	14
    "A"	0.010	0.903	0.012	0.000	0.899	0.000	0.074	0.020	0.968	0.414	0.029
    "C"	0.001	0.048	0.985	1.000	0.058	1.000	0.926	0.951	0.013	0.455	0.047
    "G"	0.980	0.049	0.000	0.000	0.008	0.000	0.000	0.007	0.006	0.066	0.860
    "T"	0.009	0.000	0.003	0.000	0.035	0.000	0.000	0.022	0.013	0.064	0.064

    "Tcf4"	1	2	3	4	5	6	7	8	9
    "A"	0.197	0.036	0.056	0.024	0.058	0.048	0.876	0.194	0.097
    "C"	0.337	0.662	0.103	0.032	0.004	0.165	0.000	0.000	0.366
    "G"	0.228	0.143	0.003	0.029	0.010	0.675	0.022	0.017	0.481
    "T"	0.238	0.159	0.837	0.915	0.929	0.112	0.099	0.782	0.056

    "cETS1"	1	2	3	4	5	6	7	8	9
    "A"	0.326	0.108	0.002	0.000	0.975	0.375	0.647	0.141	0.315
    "C"	0.345	0.842	0.000	0.002	0.003	0.078	0.046	0.354	0.300
    "G"	0.209	0.044	0.993	0.992	0.003	0.014	0.290	0.136	0.145
    "T"	0.120	0.006	0.005	0.004	0.019	0.533	0.018	0.369	0.240

    "Known mismatches with activity in vivo (GLI, Tcf4) are indicated by boxes, the degenerate high affinity sequence derived from semiquantitative SELEX analysis (c-ETS1) is indicated by green background. References:"
    	"GENE"	"Comment"				"Reference"
    "GLI1, 2, 3"	"FOXA2"	"FOXA2 requires high amounts of Shh to be induced"				"Sasaki H, Hui C, Nakafuku M, Kondoh H. A binding site for Gli proteins is essential for HNF-3beta floor plate enhancer activity in transgenics and can respond to Shh in vitro. Development 12:1313-1322, 1997."
    "Tcf4"	"CDX1"	"two binding sites mutated"				"Jho EH, Zhang T, Domon C, Joo CK, Freund JN, Costantini F. Wnt/beta-catenin/Tcf signaling induces the transcription of Axin2, a negative regulator of the signaling pathway. Mol Cell Biol. 22:1172-1183, 2002."
    "c-ETS1"	"-"	"Consensus from SELEX: (A)CMGGAWRTT"				"Woods DB, Ghysdael J, Owen MJ. Identification of nucleotide preferences in DNA sequences recognised specifically by c-Ets-1 protein. Nucleic Acids Res. 20:699-704, 1992. "