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jyyulab / SJARACNe

Scalable Tool for Gene Network Reverse Engineering
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Cannot find probe: XXXX in "tmp/XXX/tf.txt" ... ignored #20

Closed SherryDong closed 2 years ago

SherryDong commented 5 years ago

The error is as follows:

image

with input file:

tf_demo.txt

This may because the tf.txt is prepared under windows system ?

guozihuaa commented 4 years ago

The error is as follows:

image

with input file:

tf_demo.txt

This may because the tf.txt is prepared under windows system ?

Hi, have you solved this problem. I have tried to convert the tf.txt file as a unix txt format using dos2unix commond. But i still got this problem.

khughitt commented 4 years ago

Same issue here for a completely different probe list. I don't think it has anything to do with the line-encodings of the inputs files.

The issues appears to be related to this part of main.cpp, lines 224:225:

if (hub.length() == 0 || hub[0] != '_')
    hub = "_" + hub;

I'm not sure what the underscore prefix is being used for, but this is where the valid "XX" gene symbols are being converted to "_XX".

adamdingliang commented 2 years ago

I do think this is the windows end of line issue.

The issue relates to the following lines:

250 for (int i = 0; i < numTFs; i++) 251 { 252 int gid = data.getProbeId(p.tf_list[i]); 253 if (gid == -1) 254 std::cout << "Cannot find probe: " << p.tf_list[i] << " in \"" 255 << p.annotfile << "\" ... ignored." << std::endl; 256 else 257 transfac[gid] = 1; 258 }