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::Tools::Geneid(3pm) User Contributed Perl Documentation Bio::Tools::Geneid(3pm)NAME
Bio::Tools::Geneid - Results of one geneid run
SYNOPSIS
use Bio::Tools::Geneid;
my $gid = Bio::Tools::Geneid(-file => "geneid.out");
while (my $gene = $gid->next_prediction)
{
my @transcripts = $gene->transcripts;
foreach my $t (@transcripts)
{
my @exons = $t->exons;
foreach my $e (@exons)
{
printf("Exon %d..%d
", $e->start, $e->end);
}
}
}
DESCRIPTION
This is the parser for the output of geneid by Enrique Blanco and Roderic Guigo (IMIM-UPF). See http://www1.imim.es/software/geneid. It
relies on native geneid output format internally and will work with geneid versions 1.0 and 1.1. Currently this module supports only the
default mode of operation which is to predict exons and assemble an optimal gene prediction.
It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object.
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 - Keith James
Email: kdj@sanger.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $obj->new(-file = "<geneid.out");
$obj->new(-fh => *GI);
Function: Constructor for geneid wrapper. Takes either a file
: or filehandle
Returns : L<Bio::Tools::Geneid>
next_prediction
Title : next_prediction
Usage : while($gene = $geneid->next_prediction)
{
# do something
}
Function: Returns the gene structure prediction of the geneid result
file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::SeqFeature::Gene::GeneStructure object
Args : None
_add_exon
Title : _add_exon
Usage : $obj->_add_exon($gene, $transcript, ... exon data ...)
Function: Adds a new exon to both gene and transcript from the data
: supplied as args
Example :
Returns : Nothing
_set_strand
Title : _set_strand
Usage : $obj->_set_strand($gene)
Function: Sets the overall gene strand to the same strand as all
: the exons if they are all on the same strand, or to strand 0
: if the exons are on different strands.
Example :
Returns : Nothing
_target_id
Title : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns : A target ID
perl v5.14.2 2012-03-02 Bio::Tools::Geneid(3pm)
02-22-2016
.