day1_history.txt

# terminal input history for day 1 of HBEC software carpentry course
# instructor: Bret Beheim

## Navigating Files and Directories
## https://swcarpentry.github.io/shell-novice/02-filedir/index.html

ls
pwd
ls -F
ls data-shell
pwd
ls data-shell/north-pacific-gyre
ls data-shell/north-pacific-gyre/2012-07-03
ls -F data-shell/north-pacific-gyre/2012-07-03
cd data-shell
pwd
ls
cd molecules
pwd
ls
cd ..
pwd
cd ..
pwd
cd ..
pwd
cd ..
pwd
cd ..
pwd
ls -F
cd /Users/bretbeheim/Desktop/data-shell
pwd
ls
cd north-pacific-gyre/
ls
cd ..
ls
pwd
ls
cd molecules/
ls
cd ..

ls --help
man ls
man pwd
ls -l
ls
ls -l -h
ls -lh
cd ~
pwd
cd ~/Desktop
cd /Users/bretbeheim/Desktop
cd .
wd
pwd
ls

## Working With Files and Directories
## https://swcarpentry.github.io/shell-novice/03-create/index.html

cd ./data-shell
pwd
mkdir thesis
ls -F
mkdir thesis/chapter_1
mkdir thesis/chapter_1/section_1/subsection_1
mkdir -p thesis/chapter_1/section_1/subsection_1
cd thesis
nano draft.txt
ls
cat draft.txt
mv
cp
ls
mv draft.txt ch1_draft.txt
ls
cat ch1_draft.txt 
mv ch1_draft.txt chapter_1/
ls
ls chapter_1
cp ch1_draft.txt ch1_draft_copy.txt
ls
cd chapter_1
ls
cp ch1_draft.txt ch1_draft_copy.txt
ls
cat ch1_draft.txt
cat ch1_draft_copy.txt
ls
nano ch1_draft.tx
ls
nano ch1_draft.txt
cat ch1_draft.txt
rm -i ch1_draft_copy.txt
ls
rm section_1
ls
rm -r section_1

## Pipes and Filters
## https://swcarpentry.github.io/shell-novice/04-pipefilter/index.html

ls
pwd
cd ..
pwd
ls
cd data
ls
ls -F
mkdir backup
cp amino-acids.txt animals.txt backup/
ls backup
ls
ls *.txt
cd ..
ls
cd molecules
ls
ls *ethane.pdb
ls ?ethane.pdb
ls ???ane.pdb
ls
cp propane.pdb .
nano values.txt
cat values.txt
sort values.txt
sort -n values.txt
history
cd ..
pwd
history > day1_history.txt
cat day1_history.txt
cd data-shell
cd molecules
ls
cat values.txt
sort values.txt
sort -n values.txt
wc values.txt
wc -l values.txt
wc -m values.txt
wc -w values.txt
ls
cat cubane.pdb
wc cubane.pdb
wc -l *.pdb
wc -l *.pdb > lengths.txt
cat lengths.txt
sort -n lengths.txt
sort -n lengths.txt > sorted-lengths.txt
cat lengths.txt
cat sorted-lengths.txt
wc -l *.pdb > lengths.txt
sort -n lengths.txt > sorted-lengths.txt
wc -l *.pdb | sort -n
wc -l *.pdb | sort -n > sorted-lengths.txt
cat sorted-lengths.txt 
head -n 1 sorted-length.txt
head -n 1 sorted-lengths.txt
head -n 2 sorted-lengths.txt
head -n 3 sorted-lengths.txt
tail -n 1 sorted-lengths.txt
tail -n 2 sorted-lengths.txt
head -n 5 sorted-lengths.txt | tail -n 1
cat sorted-lengths.txt
wc -l *.pdb | sort -n | head -n 1
ls
pwd
cd ..
ls
cd north-pacific-gyre/
ls
cd 2012-07-03/
ls
ls -F
wc -l *.txt | sort -n | head -n 5
wc -l *.txt | sort -n | tail -n 5
ls *Z.txt
ls *[AB].txt
ls *[!AB].txt

## Loops
## https://swcarpentry.github.io/shell-novice/05-loop/index.html

cd ..
ls
cd creatures
ls
cat basilisk.dat 
head -n 10 basilisk.dat 
head -n 2 basilisk.dat | tail -n 1
ls
for filename in in basilisk.dat minotaur.dat unicorn.dat; do   head -n 2 $filename | tail -n 1; done
for filename in basilisk.dat minotaur.dat unicorn.dat; do head -n 2 $filename | tail -n 1; done
for filename in *.dat; do   head -n 2 $filename | tail -n 1; done
for filename in *.dat; do   head -n 2 $filename | tail -n 1; done > creature_classifications.txt
cat creature_classifications.txt 
for classinfo in *.dat; do   head -n 2 $classinfo | tail -n 1; done
for datinfo in *.dat; do   head -n 2 $datinfo | tail -n 1; done
for datinfo in *.dat; do   echo head -n 2 $datinfo | tail -n 1; done
cd ..
cd molecules
ls
cd ..
ls
cd north-pacific-gyre/
for datafile in NENE*[AB].txt; do   echo $datafile; done
ls
# woops, I'm in the wrong working directory
cd 2012-07-03
ls
for datafile in NENE*[AB].txt; do   echo $datafile; done
for datafile in NENE*[AB].txt; do   echo $datafile stats-$datafile; done
for datafile in NENE*[AB].txt; do bash goostats $datafile stats-$datafile; done
for datafile in NENE*[AB].txt; do   echo $datafile;   bash goostats $datafile stats-$datafile; done
echo hello there
ls -F
bash goostats NENE01729A.txt stats-NENE01729A.txt
bash goostats NENE01729B.txt stats-NENE01729B.txt

## Shell Scripts
## https://swcarpentry.github.io/shell-novice/06-script/index.html

cd ..
cd molecules
ls
rm *.txt
ls
nano middle.sh
ls
ls -F
cat middle.sh
bash middle.sh
head -n 15 octane.pdb | tail -n 5
nano middle.sh
bash middle.sh octane.pdb
bash middle.sh methane.pdb
ls
bash middle.sh cubane.pdb
cat middle.sh
nano middle.sh
bash middle.sh cubane.pdb 15 5
bash middle.sh cubane.pdb 15 2
bash middle.sh cubane.pdb 15 1
bash middle.sh cubane.pdb 15 4
./middle.sh cubane.pdb 15 4
cd ..
cd north-pacific-gyre/2012-07-03/
ls
nano do-stats.sh
cat do-stats.sh
nano do-stats.sh
cat do-stats.sh
bash do-stats.sh
cat do-stats.sh
cd ~/Desktop
history > day1_history.txt