Skip to content

Commit

Permalink
Alpha release
Browse files Browse the repository at this point in the history
  • Loading branch information
@V-Z
V-Z committed Jul 24, 2015
1 parent 8716454 commit 2747e1c
Show file tree
Hide file tree
Showing 4 changed files with 257 additions and 178 deletions.
3 changes: 0 additions & 3 deletions .gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,3 @@ src
picard.sh
tput_test.sh
problemy
contigs.tsv
sequences.fasta
git_instructions
83 changes: 83 additions & 0 deletions sondovac_functions
View file
Original file line number Diff line number Diff line change
Expand Up @@ -576,3 +576,86 @@ function workdirpath {
# Add bin directory in current directory into PATH
PATH=$PATH:$BIN
}

# Function to check and read input files
# Parameters: 1) parameter for particular file; 2) name (description) of input file; 3) variable for particular file (written into $CHECKFILEREADOUT)
function readinputfile {
echo
CHECKFILEREAD=$3
if [ "$STARTINI" == "I" ]; then
if [ -z "$CHECKFILEREAD" ]; then
echo "Provide file name for $2 input file:"
while :
do
read CHECKFILEREAD
# Test if input file is readable
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
break
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable!"
fi
done
else
echo "As input $2 file you provided via parameter ${BOLD}$1${NORM} file \"$CHECKFILEREAD\". Would you like to use it (Yes) or to provide new file (New)?"
read CHECKFILE
while :
do
case "$CHECKFILE" in
Y|y|YES|Yes|yes)
echo "Keeping \"$CHECKFILEREAD\"..."
echo
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable! Provide new one:"
while :
do
read CHECKFILEREAD
# Test if input file is readable
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
break
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable!"
fi
done
fi
break
;;
N|n|NO|No|no|NEW|New|new)
echo "Provide file name for new $2 input file:"
while :
do
read CHECKFILEREAD
# Test if input file is readable
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
break
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable!"
fi
done
break
;;
*)
echo "Wrong option. Use Y or N."
read CHECKFILE
;;
esac
done
fi
else
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable!"
exit 1
fi
fi
CHECKFILEREADOUT=$CHECKFILEREAD
}
83 changes: 0 additions & 83 deletions sondovac_part_a.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -829,89 +829,6 @@ checktools cat
# Check if perl is available
checktools perl

# Function to check and read input files
# Parameters: 1) parameter for particular file; 2) name (description) of input file; 3) variable for particular file (written into $CHECKFILEREADOUT)
function readinputfile {
echo
CHECKFILEREAD=$3
if [ "$STARTINI" == "I" ]; then
if [ -z "$CHECKFILEREAD" ]; then
echo "Provide file name for $2 input file:"
while :
do
read CHECKFILEREAD
# Test if input file is readable
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
break
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable!"
fi
done
else
echo "As input $2 file you provided via parameter ${BOLD}$1${NORM} file \"$CHECKFILEREAD\". Would you like to use it (Yes) or to provide new file (New)?"
read CHECKFILE
while :
do
case "$CHECKFILE" in
Y|y|YES|Yes|yes)
echo "Keeping \"$CHECKFILEREAD\"..."
echo
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable! Provide new one:"
while :
do
read CHECKFILEREAD
# Test if input file is readable
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
break
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable!"
fi
done
fi
break
;;
N|n|NO|No|no|NEW|New|new)
echo "Provide file name for new $2 input file:"
while :
do
read CHECKFILEREAD
# Test if input file is readable
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
break
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable!"
fi
done
break
;;
*)
echo "Wrong option. Use Y or N."
read CHECKFILE
;;
esac
done
fi
else
if [[ -f $CHECKFILEREAD && -r $CHECKFILEREAD && -s $CHECKFILEREAD ]]; then
echo
echo "Input file \"$CHECKFILEREAD\" exists and is readable. Proceeding..."
else
echo "Error! File \"$CHECKFILEREAD\" does not exist, is empty or is not readable!"
exit 1
fi
fi
CHECKFILEREADOUT=$CHECKFILEREAD
}

CHECKFILEREADOUT=""
readinputfile -f "FASTA transcriptomic data" $INPUTFILE
INPUTFILE=$CHECKFILEREADOUT
Expand Down
Loading

0 comments on commit 2747e1c

Please sign in to comment.