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Full Discussion: Printing into two files under difference situation
Top Forums UNIX for Dummies Questions & Answers Printing into two files under difference situation Post 302861393 by Smiling Dragon on Tuesday 8th of October 2013 08:59:43 PM
Old 10-08-2013
Quote:
Originally Posted by grace_shen
Thank you so much!But is it perl or shell script? I am sorry for the easy questions. I usually working on Perl, but it is not like the regular one. How can I run it? Run under the linux command line?

---------- Post updated at 07:55 PM ---------- Previous update was at 07:37 PM ----------

thank you so much for the reply, but I am really a newbie in coding, could u please add some comment on each line so that it is easy for me to refer and adjust. Thank you so much and I really appreciate all the help.
It's unix commandline, but also works in a shell script.
If you make a new file, put:
Code:
#!/bin/sh

As the first line, then the code below in it. You'll be able to run it as a script.
Otherwise, can just copy paste the entire thing into your shell on the commandline at it'll work.

Version with comments:
Code:
#Run the following for every file in the current directory that ends with ".gff" - note that it might
# get confused if you have gff files with a space in the filename.
for file in *.gff
do
  # Find the filename prefix by removing the ".gff" part of the filename
  fileprefix=`echo "$file" | sed 's/\.gff$//'`
  # Go through the .gff file line by line
  cat ${file} | while read line
  do
    # by default, assume we want to include all lines in the "yes" file
    include="yes"
    # For each word on the given line, see if it's present in "name.txt"
    for entry in $line
    do
      # If it is not present, then we know we need to put this line in the "no" file instead
      grep "$entry" name.txt > /dev/null || include=""
    done
    # If we get to the end and $include still has something in it ("yes") then we know we found all the entries on this line
    # So we add it to the "yes" file, otherwise the "no" file
    if [ -n "$include" ]
    then
      echo "${line}" >> "${fileprefix}_yes.gff"
    else
      echo "${line}" >> "${fileprefix}_no.gff"
    fi
  done
  # move onto the next line in the current .gff file
done
# move onto the next gff file

I suspect that perl would be able to do this a little more effiicently by loading the name.txt file into memory, allowing faster checks. But I usually only reach for perl if shell can't do it within a reasonable amount of time/effort.
 

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LEARN ABOUT DEBIAN

bio::graphics::glyph::vista_plot

Bio::Graphics::Glyph::vista_plot(3pm)			User Contributed Perl Documentation		     Bio::Graphics::Glyph::vista_plot(3pm)

NAME

       Bio::Graphics::Glyph::vista_plot - The "vista_plot" glyph

SYNOPSIS

       See Bio::Graphics::Glyph, Bio::Graphics::Glyph::wiggle_xyplot and Bio::Graphics::Glyph::heat_map.

DESCRIPTION

       This glyph draws peak calls (features with discreet boundaries, i.e. putative transcription sites, over signal graph (wiggle_xyplot)
       requires a special load gff file that uses attributes 'wigfile' and 'peak_type'

       Example:

       2L  chip_seq  vista  5407   23011573  .	.  .  Name=ChipSeq Exp 1;wigfile=SomeWigFile.wigdb;peak_type=binding_site:exp1

       The glyph will draw the wiggle file first, than overlay the peaks (if there are any) over signal graph. Elsewhere in the GFF3 file, there
       should be one or more features of type "binding_site:exp1", e.g.:

       2L  exp1  binding_site  91934  92005  .	.  .

       Options like 'balloon hover' and 'link' are available to customize interaction with peaks in detail view.

       BigWig support:

       Supported bigwig format also requires another attribute to be supplied in load gff file (fasta) which specifies sequence index file for the
       organism in use. The data file should have the 'bw' extension - it is used to detect the BigWig format by vista_plot

       3L  chip_seq  vista   1	  24543530  .  .  .   Name=ChipSeq Exp
       2;wigfile=SomeBigWigFile.bw;peak_type=binding_site:exp2;fasta=YourOrganism.fasta

       Note that all attributes should be present in load gff, as the code currently does not handle situation when only some of the attributes
       are in gff. To omit peak or signal drawing use "" (i.e. peak_type="") In both cases, the stanza code will look the same (only essential
       parameters shown):

	[VISTA_PLOT]
	feature 	= vista:chip_seq
	glyph		= vista_plot
	label		= 1
	smoothing	= mean
	smoothing_window = 10
	bump density	= 250
	autoscale	= local
	variance_band	= 1
	max_peak	= 255
	min_peak	= 1
	peakwidth	= 3
	start_color	= lightgray
	end_color	= black
	pos_color	= blue
	neg_color	= orange
	bgcolor 	= orange
	alpha		= 80
	fgcolor 	= black
	database	= database_with_load_gff_data
	box_subparts	= 1
	bicolor_pivot	= min
	key		= VISTA plot

OPTIONS

       Options are the same as for wiggle_xyplot and heat_map

       Additional parameters:

       alpha set transparency for peak area.

       glyph_subtype Display only 'peaks', 'signal', 'density' or 'peaks+signal'.  Aliases for 'peaks+signal' include "both" and "vista".

       Recommended global settings:

       for proper peak drawing transparency should be enabled by setting truecolors=1 in GBrowse.conf file

BUGS

       Please report them.

SEE ALSO

       Bio::Graphics::Panel Bio::Graphics::Glyph Bio::Graphics::Glyph::wiggle_xyplot Bio::Graphics::Glyph::heat_map GD

AUTHOR

       Peter Ruzanov pruzanov@oicr.on.ca

       Copyright (c) 2010 Ontario Institute for Cancer Research

	This package and its accompanying libraries is free software; you can
	redistribute it and/or modify it under the terms of the GPL (either
	version 1, or at your option, any later version) or the Artistic
	License 2.0.  Refer to LICENSE for the full license text. In addition,
	please see DISCLAIMER.txt for disclaimers of warranty.

perl v5.14.2							    2012-02-20				     Bio::Graphics::Glyph::vista_plot(3pm)
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