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BASH Scripting

A beginners guide to B ourne A gain SH ell scripting. BASH Scripting. BASH script header. On the first line #!/bin/bash - Tells the operating system that the following will be a script and not a regular text file You add - to the end to prevent users from spoofing the interpreter

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BASH Scripting

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  1. A beginners guide to Bourne Again SHell scripting BASH Scripting

  2. BASH script header • On the first line • #!/bin/bash - • Tells the operating system that the following will be a script and not a regular text file • You add - to the end to prevent users from spoofing the interpreter • Change the file to give it execute permissions • chmod +x test.sh

  3. How scripts work • #!/bin/bash -- • echo ”Hello” • ls -al • /bin/bash echo ”Hello” • /bin/bash ls -al

  4. Variables – Global vs Local • defocus=”0.5” • function defocus { • local defocus=”0.2” • echo $defocus • } • echo $defocus • Output: • 0.2 • 0.5

  5. Executing shell commands • echo ”ls -al” • echo `ls -al` • Output: • ls -al • total 16 • drwxr-x--- 2 user group 4096 2010-01-11 11:11 . • drwxr-x--- 76 user group 4096 2011-06-01 17:21 ..

  6. BASH menus • echo ”1) shorten file name” • echo ”2) convert tifs into pifs” • read -p ”selection: ” choice • case $choice in • 1 | [Ss][Hh][Oo][Rr][Tt]) echo ”you selected shorten file names” ;; • 2) echo ”you selected convert tifs” ;; • *) echo ”nothing selected” ;; • esac

  7. Test operator • curDir=`basename $PWD` • #curDir is /usr/tif • if [ ”$curDir” != ”pif” ] • then • echo ”you are not in the pif directory” • else • fi

  8. Rename a file • Input: micrograph image from bob.tif • ls *.tif | while read file • do • mv ”$file” ”`echo ”$file” | nawk ' BEGIN {OFS=”_”} $1=$1 ' ` ” • done • Exit • Output: micrograph_image_from_bob.tif

  9. Convert tifs into pifs • Directory has files 1.tif, 2.tif, etc • read -p "What is the bin factor? (1,2,3) " bin • ls -1 *.tif | awk -v bin=$bin -F. ' { newFile = $1; printf( "tiff2pif %s %s.pif %s\n", $0, newFile, bin ); }' | bash • Output: tiff2pif 1.tif 1.pif 2

  10. Shorten micrograph file name • Input: 5-26-11-ev71-Mab-dataset-120000.0V-50000X-0001.tif • ls -1 *.tif | awk -F- ' { newFile = $9; sub(/0*/, "", newFile); printf( "mv %s %s\n", $0,newFile); }' | bash • Output: 1.tif

  11. Rename box files • Input: 1_box.pif • ls -1 *box.pif | awk -F_ ' { newFile = $1; printf( "mv %s %s.pif\n", $0, newFile ); }' | bash • Output: 1.pif

  12. Change the color of pdbs • Input file: pdb • Input: x, y, z value; beginning and end value • awk -v x=$x -v y=$y -v z=$z -v beg=$beg -v end=$end ' { FIELDWIDTHS = "4 7 5 4 2 4 12 8 8 6 6 6 6" } $1=="ATOM" { NR>=beg && NR<=end; $7=x; $8=y; $9=z; print $1""$2""$3""$4""$5""$6" "$7" "$8" "$9" "$10""$11""$12""$13 } ' $pdb > color_$pdb

  13. Create dats • Input: pixel size and voltage • awk -F, ' {printf("echo \"../images/%s.pif\" > %s.dat_000\n", $1, $1) } ' defocus.csv | bash • awk -v pixDec=$pixDec -v volt=$volt -F, '{printf("echo \" %s, 1, %s000.0, 0.0700, %s, %s, 0.0000, 2.00\" >> %s.dat_000\n", pixDec, volt, $2, $2, $1) } ' defocus.csv | bash • Output: • ../images/1.pif • 4, 1, 12000.0, 0.0700, 2.5, 2.5, 0.0000, 2.00

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