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Messages - jason

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1
General Discussion / Re: Error converting PWM to PSAM
« on: December 21, 2017, 08:40:13 pm »
It works great! Thanks a ton.

2
General Discussion / Re: Error converting PWM to PSAM
« on: December 19, 2017, 02:08:41 pm »
Great! If all it takes is a simple transpose of the PFM matrix, I could handle the rest, but thank you for offering to upgrade the script! Hopefully other users in the future find it helpful.

-Jason

3
General Discussion / Re: Error converting PWM to PSAM
« on: December 19, 2017, 01:27:00 pm »
I see! I don't have much experience with the PWM format, so I thank you for looking into this.

Is the expected PWM format then only integer values, like a count matrix?

Yetfasco also provides the data as a "PFM" or Position Frequency Matrix. In this matrix, all the values are stored as fractions between 0 and 1. http://yetfasco.ccbr.utoronto.ca/1.02/Downloads/Expert_PFMs.tar.gz

The equivalent PFM to YDR146C that you pasted is this:

A       0.403846154     0.653846154     0.0     0.0     1.0     0.0     0.0     0.615384615
T       0.25    0.038461538     0.0     0.0     0.0     0.0     0.0     0.076923077
G       0.25    0.038461538     0.0     0.0     0.0     1.0     0.0     0.076923077
C       0.096153846     0.269230769     1.0     1.0     0.0     0.0     1.0     0.230769231


I also tried converting the PFM to PSAM and got an error, but perhaps I could, for example, scale each PFM to integer values from 0 to 100 and convert that?

4
General Discussion / Error converting PWM to PSAM
« on: December 18, 2017, 02:01:28 pm »
Hi, I've downloaded a set of PWMs from YeTFaSCo: http://yetfasco.ccbr.utoronto.ca/1.02/Downloads/Expert_PWMs.tar.gz

I would like to use these PWMs with the Transfactivity program.

However, I can't seem to get the convert2psam utility to work on these... I assume that it expects a slightly different PWM format than the ones provided by the download, but I can't figure out exactly what format it expects. Could you perhaps let me know if I'm doing something wrong?

Here's the command I ran and the error:

 bin/Convert2PSAM -source=pw -inp=data/yetfasco/ALIGNED_ENOLOGO_FORMAT_PWMS/YDR146C_569.pwm -pwmfile=test.xml

<data/yetfasco/ALIGNED_ENOLOGO_FORMAT_PWMS/YDR146C_569.pwm> not in PWM format: [A   0.381537584575116   1.07668300283655   -800   -800   1.68965987938785   -800   -800   0.989220160345073] contains invalid W a


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