I updated the portion of code and it does seem to append the entered genes to a file GENE.txt. The problem is even though each line is one a new line a space is put in after wach so no calculation results.
PTPN11,SCN1A,FBN1
GENE.txt looks like
.
However, if there is only one gene entered PTPN11 then the calculation works fine.
I apologize about the indenting, I am a scientist and not a programmer. Can you recommend some books on correct indentation? Thank you .
Last edited by cmccabe; 02-23-2016 at 03:17 PM..
Reason: updated code
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::Graphics::Glyph::gene(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::gene(3pm)NAME
Bio::Graphics::Glyph::gene - A GFF3-compatible gene glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph is used for drawing genes that may have alternatively-spliced transcripts. The various isoforms are stacked on top of each other
and given a single label and description that apply to the entire stack. Each individual transcript's name is optionally printed to the
left of the transcript glyph.
Transcripts (splice isoforms) are drawn using the processed_transcript glyph. CDS features are drawn in the background color, and the UTRs
are drawn in an alternate color selected by the utr_color option. In addition, you can make the UTRs thinner than the CDS by setting the
"thin_utr" option.
This glyph is designed to work properly with GFF3-style three-tier genes, in which the top level feature has the Sequence Ontology type of
"gene", the second level feature(s) have the SO type "mRNA", and the third level feature(s) have the SO type "CDS", "five_prime_utr" and
"three_prime_utr." Subparts named "UTR" are also honored. The feature can contain other subparts as well (e.g. exon, intron,
translation), but they are currently ignored unless the option sub_part is supplied. If the sub_part option is used that feature type will
be used and CDS and UTR features will be excluded. This could be used for specifying that exons be used instead, for example.
This glyph is a subclass of processed_transcript, and recognizes the same options.
OPTIONS
The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.
Option Description Default
------------------------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type undef (false)
-connector_color
Connector color black
-label Whether to draw a label undef (false)
-description Whether to draw a description undef (false)
-strand_arrow Whether to indicate undef (false)
strandedness
-hilite Highlight color undef (no color)
In addition, the gene glyph recognizes the following glyph-specific options:
Option Description Default
------------------------
-label_transcripts undef (false)
Flag. If true, then the
display name of each
transcript will be drawn
to the left of the transcript
glyph.
-thin_utr Flag. If true, UTRs will undef (false)
be drawn at 2/3 of the
height of CDS segments.
-utr_color Color of UTR segments. Gray #D0D0D0
-decorate_introns
Draw strand with little arrows undef (false)
on the intron.
The -adjust_exons and -implied_utrs options are inherited from processed_transcript, but are quietly ignored. Please use the
processed_transcript glyph for this type of processing.
BUGS
The SO terms are hard-coded. They should be more flexible and should recognize ISA relationships.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle,
Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Lincoln Stein <lstein@cshl.org>
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::gene(3pm)