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 OSF1
mhpath
mhpath(1) General Commands Manual mhpath(1)NAME
mhpath - print full pathnames of MH messages and folders (only available within the message handling system, mh)
SYNOPSIS
mhpath [+foldername] [msgs] [-help]
OPTIONS
Prints a list of the valid options to this command.
DESCRIPTION
Use the mhpath command to display the full pathname of the specified folder. If you do not specify a folder, mhpath displays the pathname
of the current folder.
If you specify a message with its message number, mhpath displays the pathname of the specified message. You can also specify a number of
messages, or a range of messages. If the top of the range that you specify is greater than the last message in the folder, mhpath displays
as much of the specified range as possible.
Additionally mhpath can take a keyword or a sequence name. The following keywords are acceptable: The first message in the folder. The
last message in the folder. The message after the last message in the folder. You cannot use new as part of a message range. The current
message in the folder. The message before the current message. The message after the current message. All of the messages in the folder.
PROFILE COMPONENTS
Path: To determine your Mail directory
EXAMPLES
In the following example, mhpath displays message 3 in the folder +inbox: % mhpath +inbox 3 /r/phyl/Mail/inbox The following example dis-
plays the pathname of messages 2 to 5 in the current folder: % mhpath 2-5 /r/phyl/Mail/inbox/2 /r/phyl/Mail/inbox/3 /r/phyl/Mail/inbox/4
/r/phyl/Mail/inbox/5
FILES
The user profile.
SEE ALSO folder(1)mhpath(1)
09-28-2016
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