Question: Split file not working
0
gravatar for jaqx008
12 days ago by
jaqx00840
jaqx00840 wrote:

For some reason split -l stopped working on my terminal or through shell script. Someone please help.

example:

split -l 1 xy.bed

it outputs xaa with all lines in xy.bed

file split unix • 119 views
ADD COMMENTlink modified 12 days ago by zx87547.5k • written 12 days ago by jaqx00840
3
gravatar for WouterDeCoster
12 days ago by
Belgium
WouterDeCoster39k wrote:

How many lines are in xy.bed? Can you show us a few of those lines?

Did you manipulate this file on Windows? If so, does dos2unix xy.bed change the results of split?

ADD COMMENTlink written 12 days ago by WouterDeCoster39k

Also worth checking is which split, and ensuring it's the actual split command one expects.

ADD REPLYlink written 12 days ago by RamRS22k

which split gave

/usr/bin/split

ADD REPLYlink written 12 days ago by jaqx00840

there are 200 lines in bed. text was made with text wrangler. it was working before were i tried to run the command with a bed file with about 6 million lines and I think it died or the command is broken or something. the out put xaa contains 200 lines as well. see few lines below

a   755386  763541
b   1260608 1268527
c   785865  793644
2   2573604 2580316
e   1828161 1833986
f   162738  168420
ADD REPLYlink modified 12 days ago • written 12 days ago by jaqx00840

Check your line endings. You should be able to use a simple sed 's/\r/\n/' file to replace any carriage returns with new lines.

ADD REPLYlink written 12 days ago by RamRS22k

My bad the file was made in excel. that may be the reason. I am about to see

ADD REPLYlink written 12 days ago by jaqx00840

This was the problem all along. Thanks for all your help

ADD REPLYlink written 11 days ago by jaqx00840
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