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POgrep large files with multiple patterns and count occurences
 

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  1. POgrep large files with multiple patterns and count occurences
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    <p>I have a large number of files with millions of lines. Then I have a two column file which is called contaminant_list. For every file I need to get number of occurrences of all patterns, always with the name of the pattern on left side and number of its occurrences on the right side.</p> <p>This command is working just fine:</p> <pre><code>while read line; do name=$(echo $line | cut -f1 -d' '); seq=$(echo $line | cut -f2 -d' '); echo -n $(date) $name "looking for $seq" &gt;&gt;adapt_contamination_log; egrep $seq $name_of_file | wc -l &gt;&gt;adapt_contamination_log; done &lt;contaminant_list.txt; </code></pre> <p>and yields in:</p> <pre><code>Thu Sep 19 23:04:38 EDT 2013 &gt;PrefixAdapter4/1 looking for GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG 0 Thu Sep 19 23:05:55 EDT 2013 &gt;PrefixAdapter4/2 looking for CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 0 Thu Sep 19 23:07:09 EDT 2013 &gt;PrefixAdapter16/1 looking for GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCCGATCTCGTATGCCGTCTTCTGCTTG 2611 </code></pre> <p>..and so on (number of patterns I am matching is quite large) Important is that pattern GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCCGATCTCGTATGCCGTCTTCTGCTTG is in my large file 2611 times.</p> <p>However, it is very slow. Is there any way to match all patterns at the same time so that the file could be read just once?</p> <p>Here is how contaminant_list.txt looks like:</p> <pre><code>TruSeqAdapter,Index12 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG IlluminaRNARTPrimer GCCTTGGCACCCGAGAATTCCA IlluminaRNAPCRPrimer AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA RNAPCRPrimer,Index1 CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA RNAPCRPrimer,Index2 CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA RNAPCRPrimer,Index3 CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA </code></pre> <p>I was thinking about writing perl script with hash, however - my experience is that inbuilt bash solutions always work better. Do you have any ideas how to do this, please?</p> <p>Thanks.</p>
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    1. PTQuestion
    1. USPerlnika
    1. USPerlnika
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    1. COWhere does `$a` come from?
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      1. POgrep large files with multiple patterns and count occurences
      1. USfedorqui
    2. COI am sorry, that's the name of the file from the outer loop which goes through all the files. I am basically interested in loop I posted which greps all the patterns from the file contaminant_list.txt against my large file.
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      1. POgrep large files with multiple patterns and count occurences
      1. USPerlnika
    3. COI am thinking that `egrep $seq $name_of_file | wc -l` could be replaced by `grep -c $seq $name_of_file`. You avoid the pipe and also use `grep` instead of `egrep` (not needed, as there are not regex).
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      1. POgrep large files with multiple patterns and count occurences
      1. USfedorqui
 

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