Bash command "Head" is not showing certain columns of my bed/csv file

Question

I have a bed file named coverage.bed. When I execute head coverage.bed, this is the beginning of what outputs:

chr start   end .   .   strand  length  CG  CA  CT  CC  TG  AG  GG
chr1    3000380 3000440 .   .   +   172 0   2   9   2
chr1    3000492 3000552 .   .   +   172 0   1   9   1
chr1    3000593 3000653 .   .   +   1055    0   4   7   4

However, when I view the file using gedit coverage.bed, I see that this is the correct first 3 lines:

chr start   end .   .   strand  length  CG  CA  CT  CC  TG  AG  GG
chr1    3000380 3000440 .   .   +   172 0   2   9   1   3   5   2
chr1    3000492 3000552 .   .   +   172 0   1   9   2   8   1   1
chr1    3000593 3000653 .   .   +   1055    0   4   7   3   6   5   4

Why is this happening? A python script outputted this file-- could it be possible that there is something wrong with the code that would lead to this error?

Edit: the output of sed -n 2p coverage.bed | hexdump -C is:

00000000  63 68 72 31 09 33 30 30  30 33 38 30 09 33 30 30  |chr1.3000380.300|
00000010  30 34 34 30 09 2e 09 2e  09 2b 09 31 37 32 09 30  |0440.....+.172.0|
00000020  09 32 09 39 09 31 09 33  09 35 09 32 0d 0a        |.2.9.1.3.5.2..|
0000002e

I find this very interesting! What does tail show you if you use it to get from the bottom to the top? — Snorik, Aug 03 '20 at 20:16
What is the output of `sed -n 2p coverage.bed | od -tx1 -An` ? — M. Nejat Aydin, Aug 03 '20 at 20:19
The output of ```sed -n 2p coverage.bed | od -tx1 -An``` is ```63 68 72 31 09 33 30 30 30 33 38 30 09 33 30 30 30 34 34 30 09 2e 09 2e 09 2b 09 31 37 32 09 30 09 32 09 39 09 31 09 33 09 35 09 32 0d 0a``` — 11thal11thal, Aug 03 '20 at 20:22
Please add output of `sed -n 2p coverage.bed | hexdump -C` to your question (no comment). This is clearer. — Cyrus, Aug 03 '20 at 20:32
I cannot reproduce the output of `head`. It seems all well on my box. — M. Nejat Aydin, Aug 03 '20 at 20:33
Definitely another carriage return issue. Does the output change when you resize the terminal window? — oguz ismail, Aug 03 '20 at 20:35
Thank you everyone! I am not sure why but now all the columns are showing with ```head```... this is something that has happened to me in the past, and I am not sure why it randomly occurs. — 11thal11thal, Aug 03 '20 at 20:36
@oguzismail I think you are right! When executing ```head``` with too small of a window size, column data goes missing (even though the headers stay). Thank you so much! — 11thal11thal, Aug 03 '20 at 20:37
Your file has DOS CRLF line-endings (`0d 0a`). Some Linux utilities do not work well with carriage returns. Suggest `dos2unix coverage.bed coverage-linux.bed` and then work with `coverage-linux.bed`. — David C. Rankin, Aug 03 '20 at 20:40
@Snorik Most likely there is no problem with `head`. This is an issue with the terminal the OP uses. — M. Nejat Aydin, Aug 03 '20 at 20:40
@M. Never used a terminal emulator that doesn't have that *issue*, which one do you use? — oguz ismail, Aug 03 '20 at 20:49
@Cyrus I don't understand how this question is a duplicate of [remove ^M characters from file using sed](https://stackoverflow.com/questions/19406418/remove-m-characters-from-file-using-sed). The CR character is not even relevant to the problem of the OP. — M. Nejat Aydin, Aug 03 '20 at 21:27
@M.NejatAydin: I voted for "Not reproducible or was caused by a typo". RavinderSingh13 voted to close with a duplicate. Unfortunately this is not differentiated in the presentation. — Cyrus, Aug 04 '20 at 04:20

Bash command "Head" is not showing certain columns of my bed/csv file

0 Answers0