from another query subtract_query.py $input1 $input2 $begin_col $end_col $output

.. class:: infomark **TIP:** This tool complements the tool in the **Operate on Genomic Intervals** tool set which subtracts the intervals of two queries. ----- **Syntax** This tool subtracts an entire query from another query. - Any text format is valid. - If both query formats are tabular, you may restrict the subtraction to specific columns **contained in both queries** and the resulting query will include only the columns specified. - The begin column must be less than or equal to the end column. If it is not, begin column is switched with end column. - If begin column is specified but end column is not, end column will default to begin_column (and vice versa). - All blank and comment lines are skipped and not included in the resulting query (comment lines are lines beginning with a # character). - Duplicate lines are eliminated from both queries prior to subtraction. If any duplicate lines were eliminated from the first query, the number is displayed in the resulting history item. ----- **Example** If this is the **First query**:: chr1 4225 19670 chr10 6 8 chr1 24417 24420 chr6_hla_hap2 0 150 chr2 1 5 chr10 2 10 chr1 30 55 chrY 1 20 chr1 1225979 42287290 chr10 7 8 and this is the **Second query**:: chr1 4225 19670 chr10 6 8 chr1 24417 24420 chr6_hla_hap2 0 150 chr2 1 5 chr1 30 55 chrY 1 20 chr1 1225979 42287290 Subtracting the **Second query** from the **First query** (including all columns) will yield:: chr10 7 8 chr10 2 10 Conversely, subtracting the **First query** from the **Second query** (including all columns) will result in an empty dataset. Subtracting the **Second query** from the **First query** (restricting to columns c1 and c2) will yield:: chr10 7 chr10 2