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
Using the following I'm trying to print the user's response to the prompt Y / N but I get nothing other than the contents of $1?
awk '{
printf($1 " ? (Y/N)")
getline myresponse < "-"
system("read myresponse")
if (myresponse == "Y")
{ print $1... (17 Replies)
I am trying to write a awk script that prompts user for input to set the FILENAME varable. I can get it set, but I think awk is not doing anything with it.
this is what I have so far
#!/usr/bin/nawk -f
BEGIN {
FILENAME = ""
printf "Enter name of file to check in : "
... (2 Replies)
Hi guys,
I am new to AWK and unix scripting. Please see below my problem and let me know if anyone you can help.
I have 2 input files (example given below)
Input file 2 is a standard file (it will not change) and we have to get the name (second column after comma) from it and append it... (5 Replies)
Hi Jim,
I have following script,i which i need to take dynamic value .
script,
nawk -v v1=grep"INT_EUR" $propertifilename | cut -d"=" -F2` -F'~' '{if (NF-1 !=v1)
{print "Error in " $0 " at line number "NR" tilde count " N-1}}' $filename
In the above script i want to use INT_EUR as a variable... (2 Replies)
Hi,
echo "Enter file name of input file list along with absolute path : "
read inputFileList
if
then
for string in `cat inputFileList`
do
echo $string
done
else
echo " file does not exist"
fi
From the above code, if the user enters a invalid file... (1 Reply)
this section of the awk code i have here takes file to work with from the user.
the user specifies the file name from the command line and the file name is assigned to the variable $FLIST
awk 'BEGIN {
while((getline < "'${FLIST}'")>0)
S
FS="\n"; RS="}\n"
}
now, i dont want... (5 Replies)
Hello,
I'm trying to figure out how best to approach this script, and I have very little experience, so I could use all the help I can get. :wall:
I regularly need to delete files from many directories.
A file with the same name may exist any number of times in different subdirectories.... (3 Replies)
Dear Friends,
I am looking for a shell script to merge input files into one file .. here is my idea:
1st paramter would be outfile file (all input files content)
read all input files and merge them to input param 1
ex: if I pass 6 file names to the script then 1st file name as output file... (4 Replies)
Bio::SeqFeature::Gene::GeneStructureI(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::GeneStructureI(3pm)NAME
Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily
complex structure of a gene
SYNOPSIS
#documentation needed
DESCRIPTION
A feature representing a gene structure.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar Lapp
Email hlapp@gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
transcripts
Title : transcripts()
Usage : @transcripts = $gene->transcripts();
Function: Get the transcript features/sites of this gene structure.
See Bio::SeqFeature::Gene::TranscriptI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects
representing the promoter regions or sites.
Args :
promoters
Title : promoters()
Usage : @prom_sites = $gene->promoters();
Function: Get the promoter features/sites of this gene structure.
Note that OO-modeling of regulatory elements is not stable yet.
This means that this method might change or even disappear in a
future release. Be aware of this if you use it.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
promoter regions or sites.
Args :
exons
Title : exons()
Usage : @exons = $gene->exons();
@inital = $gene->exons('Initial');
Function: Get all exon features or all exons of specified type of this gene
structure.
Refer to the documentation of the class that produced this gene
structure object for information about the possible types.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
representing the exon regions.
Args : An optional string specifying the type of the exon.
introns
Title : introns()
Usage : @introns = $gene->introns();
Function: Get all introns of this gene structure.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
introns.
Args :
poly_A_sites
Title : poly_A_sites()
Usage : @polyAsites = $gene->poly_A_sites();
Function: Get the poly-adenylation features/sites of this gene structure.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
poly-adenylation regions or sites.
Args :
utrs
Title : utrs()
Usage : @utr_sites = $gene->utrs();
Function: Get the UTR features/sites of this gene structure.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
representing the UTR regions or sites.
Args :
perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::GeneStructureI(3pm)
02-22-2016
.