Bash to select oldest folder in directory automatically and log process
The `bash` below uses the oldest folder in the specified directory and logs it. The goes though an analysis process and creates a log. My problem is that if there are 3 folders in the directory folder1,folder2,folder3, the bash is using folder2 for the analysis eventhough folder1 is the oldest folder in the directory. Is the find command missing something? Also, is there a better way to log the folder used? That portion is in bold. Thank you .
Bash
Code:
#!/bin/bash
dir=/home/cmccabe/Desktop/NGS/test
{
read -r -d $'\t' time && read -r -d '' foldername
} < <(find "$dir" -maxdepth 1 -mindepth 1 -printf '%T+\t%P\0' | sort -z -r )
printf "The oldest folder is $foldername, created on $time" "and will be used for analysis on $(date "+%D %r")" >> /home/cmccabe/Desktop/NGS/test/log.txt
logfile=/home/cmccabe/Desktop/NGS/test/$foldername/process.log
for f in /home/cmccabe/Desktop/NGS/test/$foldername/bedtools/*.txt ; do
echo "Start BedTools target base depth creation: $(date) - File: $f"
bname=`basename $f`
pref=${bname%%.txt}
awk '{ sum += $7; n++ } END { if (n > 0) print sum / n; }' $f > /home/cmccabe/Desktop/NGS/test/$foldername/bedtools/${pref}_depth.bed
echo "End BedTools target base depth creation: $(date) - File: $f"
done >> "$logfile"
edit: I must have had a typo as it seems fine now... thank you .
Last edited by cmccabe; 09-29-2016 at 05:37 PM..
Reason: added edit
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Discussion started by: cmccabe
19 Replies
LEARN ABOUT REDHAT
new
NEW(1) [nmh-1.5] NEW(1)NAME
new - report on folders with new messages
fnext - set current folder to next folder with new messages
fprev - set current folder to previous folder with new messages
unseen - scan new messages in all folders with new messages
SYNOPSIS
new [sequences] [-mode mode] [-folders foldersfile] [-version] [-help]
fnext is equivalent to new -mode fnext
fprev is equivalent to new -mode fprev
unseen is equivalent to new -mode unseen
DESCRIPTION
New in its default mode produces a one-line-per-folder listing of all folders containing messages in the listed sequences or in the
sequences listed in the profile entry "Unseen-Sequence". Each line contains the folder, the number of messages in the desired sequences,
and the message lists from the .mh_sequences file. For example:
foo 11.* 40-50
bar 380. 760-772 824-828
total 391.
The `*' on foo indicates that it is the current folder. The last line shows the total number of messages in the desired sequences.
New crawls the folder hierarchy recursively to find all folders, and prints them in lexicographic order. Override this behavior by provid-
ing foldersfile containing the pre-sorted list of folders new should check, one per line.
In fnext and fprev modes, new instead changes to the next or previous matching folder, respectively.
In unseen mode, new executes scan sequences for each matching folder.
FILES
$HOME/.mh_profile The user profile
PROFILE COMPONENTS
Path: To determine the user's nmh directory
Current-Folder: To find the default current folder
Unseen-Sequence: The name of the unseen message sequence
SEE ALSO scan(1), mh-format(5)HISTORY
Based on Luke Mewburn's new (http://www.mewburn.net/luke/src/new).
MH.6.8 11 June 2012 NEW(1)
09-28-2016
.