I've been running some analyses, the results of which have been stored in a sequential manner with a directory structure like step0, step1, step2, ... for iterations 0-2, for example. Each iteration contains several nested folders, with three pieces of information I need. I need to do the following:
(1) Find within each iteration directory, and extract sequentially to a new file, the number following the text, "final GAMMA-based Likelihood:" The numbers need to be in a list whose order preserves the original order (iteration 0, 1, 2, ...).
(2) Find, copy, and concatenate into a single file the contents of the file "RAxML_bestTree.default." As for (1), the order should preserve the iteration order.
(3) Copy the file "input.phy" to a new directory called alignments, preserving the order of the iterations, and renaming the file to correspond to the iteration number, e.g. input.phy.0, inpout.phy.1, etc.
I anticipate this will require some grep and for loops, but I am very much unsure of how to proceed.
where information is actually stored in an unspecified number of files inside each step<N>subdir<M> directory; can we assume the files are ordered by filename in the order the information is to be searched and (if found) retrieved?
If this is the case, the command to list the files paths, keeping at the same time the alphabetical order of subdirs and filenames:
Code:
find JDenton/ -type f | sort
The output of the command should resemble something like this:
You may redirect the output of the above command to a file in order to keep it for reference during the current search and extraction job:
Code:
if [ -f /parent/directory/filelist.txt ] ; then
rm -f /parent/directory/filelist.txt
fi
find JDenton/ -type f | sort >> /parent/directory/filelist.txt
I think this is the core of your task, having an alphanumerically ordered list of files.
B. once you have the alphabetically ordered list you may start to look for the entries "final GAMMA-based Likelihood:" in the files:
Code:
for currentfile in `cat /parent/directory/filelist.txt`
do
# assuming that the searched string appears in a single line
# and that the number appears after the colon,
# and that there is a single colon in the line
egrep "final GAMMA-based Likelihood:" ${currentfile} | awk -F":" ' { print $2 } ' >> /parent/directory/GAMMA-numbers.txt
done
C. similar concept for your (2) bullet element:
Code:
for currentfile in `cat /parent/directory/filelist.txt | egrep "RAxML_bestTree.default"`
do
cat ${currentfile} >> /parent/directory/singlefile.txt
done
D. for bullet (3) task, you should be able to do it by yourself at this point =)
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