I have a bed file of three columns, and I would like to add the following headers: (chr \t start \t stop). I tried using the following command
echo -e "chr\tstart\tstop" | cat - myfile.bed > /tmp/out && mv /tmp/out myfile.bed
But every time I run this I get the follwoing error: cat: myfile.bed: No such file or directory
Although I'm sure the file is in that directory with the same name.
What edits I can make to let this work? or if you know another way of adding a header to a tab delimited bed file, please suggest.
Related
I have a problem. I have created a few files txt in directory.
file1.txt
file2.txt
file3.txt
Next I writing name files to file txt: filenames.txt with step: Shell.
ls D:\test\prep\ > filename.txt
I have there all name files which are in directory. My filenames.txt looks like this:
file1.txt
file2.txt
file3.txt
Later I read the values from the file in step Text file input and value which I get I writing to step copy to result.
Next I use get rows from result and transformation_executor.
I would like get a new name file for each file with step get rows from result: instead file1.txt I want file.txt. I think that in transformation_executor I must have TABLE_INPUT with name with step get rows from result but I don't know what's next.
Any have idea?
You need to use below step/way, if you want to read a directory files based on another configuration file (which contain the directory files information).
Step-1:
Step-2:
Step-3:
You can found the all transformation/Job from HERE
Please let me know if its ok with you.
I have multiple files starting with DUMP_*.
Each file has data for a particular dump.
I want to print filename as well as contents of file in stdout
The expected output should be
FILENAME
ALL CONTENTS OF FILE
and so on
Closest thing I have tried is
cat $(ll DUMP_* | awk -F ' ' '{print $9}' ) | less
With this I am not able to figure out which content belongs to which file.
Also, I am reluctant to use a shell script, an adhoc command is preferred.
This answer is not fully in line with your expectations, but you see the link between a filename and its content even better:
Situation:
Prompt>cat DUMP_1
Info
More Info
Prompt>cat DUMP_2
Info
Solution:
Prompt>grep "" DUMP_*
DUMP_1:Info
DUMP_1:More Info
DUMP_2:Info
I have a directory which contains multiple file (~1000) with names in the form of ABC.txt, ABC.1.txt, ABC.2.txt, XYZ.txt, XYZ.1.txt and so on.. I want to consider these names based on the first index if we split them by .. For example then names will be read as ABC XYZ and so on.. Then I want to remove those files for which these first index does not exist in an other (reference file). Given the file names mentioned above, let's say my other (reference file) only contains 1 name and that is XYZ. So the files that will be kept in the directory will be XYZ.txt and XYZ.1.txt and everything else which does not have the exact prefix as XYZ will be removed. I said exact because it might happen that there will be a file with name XYZA.txt, so there should be an exact match in order to keep that file.
Can anybody help me with this. Thank you very much.
EDIT: One directory contains all the files: ABC.txt, ABC.1.txt, ABC.2.txt, XYZ.txt, XYZ.1.txt and the reference file is in another directory as file name reference.txt and is a one-column file containing other directory's file (prefix)names as ABC, XYZ, CDE etc..
try
for f in *.*;
do if grep -qF "${f%%.*}" file;
then echo "skip $f";
else echo "rm $f"; fi;
done
searches all files with a dot in file name, extract the prefix until the first dot, compare literally in the file with not to be deleted names, and echo the rm file command. Make sure your file with names doesn't have a dot, otherwise it will be removed as well.
if looks fine remove echo before rm.
I have 3 groups of photos, from 3 different cameras (with time sychronised onboard all cameras) but with different naming schemes (e.g.: IMG_3142.jpg, DCM_022.jpg). I would like to rename every photo file with the following naming convention:
1_yyyy_mm_dd_hh_mm_ss.jpg for earliest
2_yyyy_mm_dd_hh_mm_ss.jpg for next earliest, and so on,
until we reach around 5000_yyyy_mm_dd_hh_mm_ss.jpg for the last one (i.e. the most recent)
I would like the yyyy_mm_dd_hh_mm_ss field to be replaced by the “date and time taken” value for when this photo was taken. Which is saved in the metadata/properties of each file.
I have seen awk used to carry out similar operations but I'm not familiar enough to know how to access the “time taken” metadata, etc.
Also, not that this should make a difference: my computer is a mac.
You can use jhead for this. The command is:
jhead -n%Y_%m_%d_%H_%M_%S *.jpg
Make a COPY of your files first before running it! You can install jhead with homebrew using:
brew install jhead
Or, if you don't have homebrew, download here for OS X.
That will get you the date in the filename as you wish. The sequence number is a little more difficult. Try what I am suggesting above and, if you are happy with that, we can work on the sequence number maybe. Basically, you would run jhead again to set the file modification times of your files to match the time they were shot - then the files can be made to show up in the listing in date order and we can put your sequence number on the front.
So, to get the file's date set on the computer to match the time it was taken, do:
jhead -ft *.jpg
Now all the files will be dated on your computer to match the time the photos were taken. Then we need to whizz through them in a loop with our script adding in the sequence number:
#!/bin/bash
seq=1
# List files in order, oldest first
for f in $(ls -rt *jpg)
do
# Work out new name
new="$seq_$f"
echo Rename $f as $new
# Remove "#" from start of following command if things look good so the renaming is actually done
# mv "$f" $new"
((seq++))
done
You would save that in your HOME directory as renamer, then you would go into Terminal and make the script executable like this:
chmod +x renamer
Then you need to go to where your photos are, say Desktop\Photos
cd "$HOME/Desktop/Photos"
and run the script
$HOME/renamer
That should do it.
By the way, I wonder how wise it is to use a simple sequence number at the start of your filenames because that will not make them come up in order when you look at them in Finder.
Think of file 20 i.e. 20_2015_02_03_11:45:52.jpg. Now imagine that files starting with 100-199 will be listed BEFORE file 2o, also files 1000-1999 will also be listed before file 20 - because their leading 1s come before file 20's leading 2. So, you may want to name your files:
0001_...
0002_...
0003_...
...
0019_...
0020_...
then they will come up in sequential order in Finder. If you want that, use this script instead:
#!/bin/bash
seq=1
for f in $(ls -rt *jpg)
do
# Generate new name with zero-padded sequence number
new=$(printf "%04d_$f" $seq)
echo Rename $f as $new
# Remove "#" from start of following command if things look good so the renaming is actually done
# mv "$f" $new"
((seq++))
done
I have a number of files created by a program on our selling system that are produced in a format like the following:
CRY_SKI_14_EDI.LIS
CRY_SUM_14_EDI.LIS
THO_SKI_14_EDI.LIS
THO_LAK_14_EDI.LIS
CRY_SKI_IE_14_EDI.LIS
These files differ in numbers depending on the split of our product to different brandings. Is it possible to rename them all so that they read like the following:
CRY_SKI_14_EDI_DEMO.LIS
CRY_SUM_14_EDI_DEMO.LIS
THO_SKI_14_EDI_DEMO.LIS
THO_LAK_14_EDI_DEMO.LIS
CRY_SKI_IE_14_EDI_DEMO.LIS
I need the files to be correctly named prior to their FTP as a hardcoded file could potentially not exist due to the brand not being on sale and terminate the FTP which would prevent the other files following it from being transmitted to our FTP server.
The OpenVMS rename command is more handy (imho) than the windows or unix variants, because it can bulk change chuncks of the full file name. Such as 'name', 'type' or (sub)directory.
For example:
$ rename *.dat *.old
That's great but it will not change within the chunks (components) like the name part requested here.
For that, the classic DCL approach is a quick loop, either parsing directory output (Yuck!) or using F$SEARCH. For example:
$loop:
$ file = f$search("*EDI.LIS")
$ if file .eqs. "" then exit
$ name = f$parse(file,,,"name","syntax_only") ! grab name component from full name
$ rename/log 'file' 'name'_demo ! rename 'fills in the blanks'
$ goto loop
Personally I use PERL one-liners for this kind of work.
(and I test with -le using 'print' instead of 'rename' first. :-)
$ perl -e "for (<*edi.lis>) { $old = $_; s/_edi/_edi_demo/; rename $old,$_}"
Enjoy!
Hein