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general:computerenvironment:bash [2023/04/11 13:16] – felixgeneral:computerenvironment:bash [2023/04/11 13:17] (current) – felix
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-''awk -F "\t" '$3 > 10 {print $0}'''+<code>awk -F "\t" '$3 > 10 {print $0}'</code>
  
   * You can indicate you want only the rows in which a column meets certain condition. For example, the column 3 requires a value greater than 10.   * You can indicate you want only the rows in which a column meets certain condition. For example, the column 3 requires a value greater than 10.
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 === Sort === === Sort ===
  
-sort -g -u file.txt+<code>sort -g -u file.txt</code>
  
   * -r to sort in descending order   * -r to sort in descending order
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 === Translate === === Translate ===
  
-tr '[ATGC]' '[TACG]' | rev+<code>tr '[ATGC]' '[TACG]' | rev</code>
  
   * This is a trick if you are working on the complementary strand.   * This is a trick if you are working on the complementary strand.
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 === sed (slightly more advanced) === === sed (slightly more advanced) ===
  
-sed -n -e '/AAA/,/BBB/ p' file.txt+<code>sed -n -e '/AAA/,/BBB/ p' file.txt</code>
  
   * This will find AAA, and keep all the lines in a file until it reaches BBB. Pro tip: use this one to extract a sequence in a multi-line fasta.   * This will find AAA, and keep all the lines in a file until it reaches BBB. Pro tip: use this one to extract a sequence in a multi-line fasta.
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 To compare contents of both files (in this case, the identifiers of the first column of the two files): To compare contents of both files (in this case, the identifiers of the first column of the two files):
  
-''comm <() <()''+<code>comm <() <()</code>
  
   * Within each "<()" we place the command of the input to compare.   * Within each "<()" we place the command of the input to compare.
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   * I use the second part of the command (the sed) to adjust the output to have the correct number of columns   * I use the second part of the command (the sed) to adjust the output to have the correct number of columns
  
-''comm <(cut -f1 1_table.txt | sort) <(cut -f1 2_table.txt | sort) | sed -e 's/$/\t\t/' | cut -f1,2,3''+<code>comm <(cut -f1 1_table.txt | sort) <(cut -f1 2_table.txt | sort) | sed -e 's/$/\t\t/' | cut -f1,2,3</code>
  
   * Output:   * Output:
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 Join two tables based on a column in common. Join two tables based on a column in common.
  
-''join -t $'\t' <() <()''+<code>join -t $'\t' <() <()</code>
  
   * Input within the "<()" must be sorted out.   * Input within the "<()" must be sorted out.
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   * The standard output will display only lines with columns in common. We can add option -a1 or -a2 to also include the entries of one of the tables, with no joined values from other. Do not use both.   * The standard output will display only lines with columns in common. We can add option -a1 or -a2 to also include the entries of one of the tables, with no joined values from other. Do not use both.
  
-''join -t $'\t' -a1 <(sort -k1,1 1_table.txt) <(sort -k1,1 2_table.txt)''+<code>join -t $'\t' -a1 <(sort -k1,1 1_table.txt) <(sort -k1,1 2_table.txt)</code>