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Published 20 hours ago • verified publisher icon wdecoster

Input file not recognized

Open KloostermanJoukje opened this issue 1 year ago • 5 comments

Hello,

I was trying out methplotlib, and my input data was a bedgraph file generated by Modkit. However, i am getting an input file not recognized message. Do you have any idea how to fix this?

This was my command: methplotlib -m ./h_CG0_positive.bedgraph -n 20231004_1422_X2_FAW14788_8e4bf9c0 -w chr7:5,525,542-5,543,028

KloostermanJoukje avatar Nov 21 '23 08:11 KloostermanJoukje

Could you share a few lines of your file?

wdecoster avatar Nov 21 '23 09:11 wdecoster

Here are a few files: (No header)

1 12331 12332 0 2 1 12355 12356 0 2 1 12426 12427 0 2 1 12506 12507 0 3 1 12521 12522 0.33333334 3 1 12558 12559 0 3 1 12586 12587 0 3 1 12672 12673 0 4

KloostermanJoukje avatar Nov 21 '23 09:11 KloostermanJoukje

I have a similar issue with my bed file

I ran modkit with the --only-tabs option, but the file was not recognized. A few lines from the file: (No header)

1       10468   10469   h       1       +       10468   10469   255,0,0 1       0.00    0       0       1       1       0       0       0
1       10468   10469   m       1       +       10468   10469   255,0,0 1       100.00  1       0       0       1       0       0       0
1       10469   10470   h       2       -       10469   10470   255,0,0 2       0.00    0       1       1       0       0       0       0
1       10469   10470   m       2       -       10469   10470   255,0,0 2       50.00   1       1       0       0       0       0       0
1       10471   10472   h       1       -       10471   10472   255,0,0 1       0.00    0       0       1       0       0       0       0

My command used:

methplotlib -m /test.bed -n test -w chrX:146,991,437-147,034,645

KloostermanJoukje avatar Nov 23 '23 11:11 KloostermanJoukje

@wdecoster

I have been comparing the utils.py file, and it seems that my version (installed using pip) is deprecated...

Any idea why using pip to install, does not yield the latest version as seen on guthub?

I also see that the version using conda is from 1 year and 7 months ago, so i suppose using that to download wont help much.

KloostermanJoukje avatar Nov 23 '23 14:11 KloostermanJoukje

@wdecoster can you help me??

Could you update methplotlib for pip installation and/or conda?

KloostermanJoukje avatar Nov 29 '23 12:11 KloostermanJoukje