Shell Programming and Scripting

uname -a
uname --all
awk
awk --version

echo Please input gene name you wish to look for
read GENE
OUT="$GENE$(date '+%Y%m%d').txt"
echo "The output file is $OUT"
for file in *.txt
do
  awk -vNAME=$GENE '$13 ~ NAME { print FILENAME": "$0 }' $file >> $OUT
done

$
$
$ cat file1.txt
chr_name        chr_start       chr_end ref_base        alt_base        hom_het snp_quality     tot_depth       alt_depth       dbSNP   dbSNP131     freqlenomes
chr01   14907   14907   A       G       het     108     52      39      snp131  rs6682375       ncRNA   WASH7P  .       .       rs6682375       .    .
chr01   14930   14930   A       G       het     148     62      44      snp131  rs6682385       ncRNA   WASH7P  .       .       rs6682385       1000g0.71nov_all
chr01   761752  761752  C       T       hom     225     69      69      snp131  rs1057213       ncRNA   NCRNA00115      .       .       rs1057213    0.5442010nov_all
chr01   761800  761800  A       T       hom     42      11      11      snp131  rs1064272       ncRNA   NCRNA00115      .       .       rs1064272    0.1142010nov_all
$
$
$ cat file2.txt
chr_name        chr_start       chr_end ref_base        alt_base        hom_het snp_quality     tot_depth       alt_depth       dbSNP   dbSNP131     freqlenomes
chr01   17556   17556   C       T       het     43      30      9       .       .       ncRNA   WASH7P  .       .       .       .       .
chr01   69511   69511   A       G       hom     225     106     106     snp131  rs2691305       exonic  OR4F5   nonsynonymous   SNV     "OR4F5:NM_0010.7892010nov_all421G:p.T141A,"
chr01   761732  761732  C       T       hom     225     103     102     snp131  rs2286139       ncRNA   NCRNA00115      .       .       rs2286139    0.5372010nov_all
$
$
$ cat search.sh
echo Please input gene name you wish to look for
read GENE
OUT="$GENE$(date '+%Y%m%d').txt"
echo "The output file is $OUT"
for file in *.txt
do
  awk -vNAME=$GENE '$13 ~ NAME { print FILENAME": "$0 }' $file >> $OUT
done
$
$
$ # Now run the script
$
$ . search.sh
Please input gene name you wish to look for
WASH7P
The output file is WASH7P20110914.txt
$
$ # Display the content of the output file
$
$ cat WASH7P20110914.txt
file1.txt: chr01        14907   14907   A       G       het     108     52      39      snp131  rs6682375       ncRNA   WASH7P  .       .       rs668.375
file1.txt: chr01        14930   14930   A       G       het     148     62      44      snp131  rs6682385       ncRNA   WASH7P  .       .       rs6680.71g2010nov_all
file2.txt: chr01        17556   17556   C       T       het     43      30      9       .       .       ncRNA   WASH7P  .       .       .       .    .
$
$
$

echo Please input gene name you wish to look for
read GENE
OUT="$GENE$(date '+%Y%m%d').txt"
echo "The output file is $OUT"
for file in *.txt
do
  perl -F"\t" -lane "print \"\$ARGV:\$_\" if \$F[12] eq $GENE" $file >> $OUT
done

$
$
$ rm WASH7P20110914.txt
$
$ # Display the script content
$
$ cat search1.sh
echo Please input gene name you wish to look for
read GENE
OUT="$GENE$(date '+%Y%m%d').txt"
echo "The output file is $OUT"
for file in *.txt
do
  perl -F"\t" -lane "print \"\$ARGV:\$_\" if \$F[12] eq $GENE" $file >> $OUT
done
$
$
$ # Now run the script
$
$ . search1.sh
Please input gene name you wish to look for
WASH7P
The output file is WASH7P20110914.txt
$
$
$ # Display the content of the output file
$
$ cat WASH7P20110914.txt
file1.txt:chr01 14907   14907   A       G       het     108     52      39      snp131  rs6682375       ncRNA   WASH7P  .       .       rs6682375    .
file1.txt:chr01 14930   14930   A       G       het     148     62      44      snp131  rs6682385       ncRNA   WASH7P  .       .       rs6682385    0.71g2010nov_all
file2.txt:chr01 17556   17556   C       T       het     43      30      9       .       .       ncRNA   WASH7P  .       .       .       .       .
$
$
$

$ uname -a
Darwin anzac-172-16-75-136.anzac.edu.au 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
$ uname --all
uname: illegal option -- -
usage: uname [-amnprsv]
$ awk
usage: awk [-F fs] [-v var=value] [-f progfile | 'prog'] [file ...]
$ awk --version
awk version 20070501

$ uname -a
Linux neuro.anzac.edu.au 2.6.18-238.5.1.el5 #1 SMP Mon Feb 21 05:52:39
EST 2011 x86_64 x86_64 x86_64 GNU/Linux
$ uname --all
Linux neuro.anzac.edu.au 2.6.18-238.5.1.el5 #1 SMP Mon Feb 21 05:52:39
EST 2011 x86_64 x86_64 x86_64 GNU/Linux
$ awk
Usage: awk [POSIX or GNU style options] -f progfile [--] file ...
Usage: awk [POSIX or GNU style options] [--] 'program' file ...
POSIX options:          GNU long options:
       -f progfile             --file=progfile
       -F fs                   --field-separator=fs
       -v var=val              --assign=var=val
       -m[fr] val
       -W compat               --compat
       -W copyleft             --copyleft
       -W copyright            --copyright
       -W dump-variables[=file]        --dump-variables[=file]
       -W exec=file            --exec=file
       -W gen-po               --gen-po
       -W help                 --help
       -W lint[=fatal]         --lint[=fatal]
       -W lint-old             --lint-old
       -W non-decimal-data     --non-decimal-data
       -W profile[=file]       --profile[=file]
       -W posix                --posix
       -W re-interval          --re-interval
       -W source=program-text  --source=program-text
       -W traditional          --traditional
       -W usage                --usage
       -W version              --version

To report bugs, see node `Bugs' in `gawk.info', which is
section `Reporting Problems and Bugs' in the printed version.

gawk is a pattern scanning and processing language.
By default it reads standard input and writes standard output.

Examples:
       gawk '{ sum += $1 }; END { print sum }' file
       gawk -F: '{ print $1 }' /etc/passwd
$ awk --version
GNU Awk 3.1.5
Copyright (C) 1989, 1991-2005 Free Software Foundation.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
02110-1301, USA.

$ ./3SNPs_in_gene.sh 
Please input gene name you wish to look for
WASH7P
The output file is WASH7P20110915.txt
awk: invalid -v option

awk: invalid -v option

awk: invalid -v option

awk: invalid -v option

awk: invalid -v option

awk: invalid -v option

awk: invalid -v option

$

echo Please input gene name you wish to look for
read GENE
OUT="$GENE$(date '+%Y%m%d').txt"
echo "The output file is $OUT"
for file in *.txt
do
  perl -F"\t" -lane "print \"\$ARGV:\$_\" if \$F[12] eq $GENE" $file >> $OUT
done

awk -v NAME="${VAR}"

awk -v pattern="WASH7P" '$13 ~ pattern {print FILENAME":"$0}' file1.txt file2.txt > out.txt

grep WASH7P file1.txt file2.txt >> out.txt

echo Please input gene name you wish to look for
read GENE
OUT="$GENE$(date '+%Y%m%d').txt"
echo "The output file is $OUT"
for file in *.txt
do
  awk -v NAME="$GENE" '$13 ~ NAME { print FILENAME": "$0 }' $file >> $OUT
done

#your original file showed this and a normal grep SOX was not working on this
root@bt:/tmp# file file1.txt 
file1.txt: Little-endian UTF-16 Unicode text, with very long lines, with CRLF line terminators

#then I opened it in gedit and saved it once again with Character Encoding as "Current Locale UTF-8" and then it started working.
root@bt:/tmp# gedit file1.txt 
root@bt:/tmp# file file1.txt 
file1.txt: ASCII text, with very long lines, with CRLF line terminators