I am trying to allow a user to enter in text and then store that text in a variable $gene to run in an awk command in which those values are used to run some calculations. I am getting syntax errors however, when I try. Thank you .
The awk runs great if it is a pre-defined file that is used, but it could also be user input.
Code:
/home/cmccabe/Desktop/loop.sh: line 87: syntax error near unexpected token `for'
/home/cmccabe/Desktop/loop.sh: line 87: `for f in /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/*base_counts.txt ; do'
Code:
other() {
printf "\n\n"
printf "Please enter the gene(s) of interest, use a comma between multiple: "; IFS="," read -a gene
printf "the indicated genes will now be loaded and used to calculate coverage\n"
[ -z "$gene" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && return
[ "$gene" = "end" ] && printf "\n Leaving match function." && sleep 2 && return
for ((i=0; i<${#gene[@]}; i++))
logfile=/home/cmccabe/Desktop/NGS/API/2-12-2015/process.log
for f in /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/*base_counts.txt ; do
echo "Start custom panel creation: $(date) - File: $f"
bname=$(basename $f)
pref=${bname%%.txt}
awk '
NR == FNR {input[$0]; next}
{
split($5, a, "-")
if (a[1] in input) {
key = $4 OFS $5
n[key]++
sum[key] += $7
}
}
END {
for (key in n)
printf "%s %.1f\n", key, sum[key]/n[key]
}
' /home/cmccabe/Desktop/panels/$gene $f | awk '{split($2,a,"-"); print a[1] "\t" $0}' | sort | cut -f2-> /home/cmccabe/Desktop/NGS/API/2-12-2015/bedtools/${pref}_genescoverage.bed
echo "End custom panel creation: $(date) - File: $f"
done >> "$logfile"
printf "coverage calculated and log created\n"
}
Last edited by cmccabe; 02-22-2016 at 06:00 PM..
Reason: updated format
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script,
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S
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GO::Model::GeneProduct(3pm) User Contributed Perl Documentation GO::Model::GeneProduct(3pm)NAME
GO::Model::GeneProduct - gene product in a particular species
DESCRIPTION
represents a gene product in a particular species (this will effectively always be refered to implicitly by the gene symbol even though a
gene may have >1 product)
acc
Usage -
Returns -
Args -
symbol
Usage -
Returns -
Args -
type
Usage -
Returns -
Args -
full_name
Usage -
Returns -
Args -
as_str
Usage -
Returns -
Args -
add_synonym
synonym_list
accessor: gets/set list of synonyms [array reference]
speciesdb
Usage -
Returns -
Args -
add_seq
Usage -
Returns -
Args - GO::Model::Seq
seq_list
Usage -
Returns - GO::Model::Seq listref
Args -
seq
Usage -
Returns - GO::Model::Seq
Args -
returns representative sequence object for this product
properties
Usage -
Returns - hashref
Args - hashref
set_property
Usage - $sf->set_property("wibble", "on");
Returns -
Args - property key, property scalar
note: the property is assumed to be multivalued, therefore
$sf->set_property($k, $scalar) will add to the array, and
$sf->set_property($k, $arrayref) will set the array
get_property
Usage -
Returns - first element of the property
Args - property key
get_property_list
Usage -
Returns - the property arrayref
Args - property key
to_fasta
Usage -
Returns -
Args -
returns the longest seq by default
perl v5.14.2 2013-02-07 GO::Model::GeneProduct(3pm)
02-22-2016
.