title: Using grep with pattern file to count individual pattern matches in a file
body: <p>I am using grep with a file that have multiple search patterns. As output I would like to get the matching pattern and the number of occurrences for that specific pattern.</p>
  
  <pre><code>cat pattern.txt
  
  AT3G09260.1
  AT5G50920.1
  </code></pre>
  
  <p>The input file looks like this</p>
  
  <pre><code>&gt;AT2G44750.1 | Symbols: TPK2 | thiamin pyrophosphokinase 2 | chr2:18451510-18452754 FORWARD LENGTH=265
  &gt;AT2G47140.1 | Symbols:  | NAD(P)-binding Rossmann-fold superfamily protein | chr2:19350970-19352059 REVERSE LENGTH=257
  &gt;AT2G47120.1 | Symbols:  | NAD(P)-binding Rossmann-fold superfamily protein 
  &gt;AT1G21470.1 | Symbols:  | BEST Arabidopsis thaliana protein match is: CLPC homologue 1 (TAIR:AT5G50920.1); Has 326 Blast hits to 324 proteins in 95 species: Archae - 0; Bacteria - 130; Metazoa - 0; Fungi - 0; Plants - 67; Viruses - 0; Other Eukaryotes - 129 (source: NCBI BLink). | chr1:7516709-7517179 REVERSE LENGTH=118
  &gt;AT3G09260.1 | Symbols: PYK10, PSR3.1, BGLU23, LEB | Glycosyl hydrolase superfamily protein | chr3:2840657-2843730 REVERSE LENGTH=524
  &gt;AT5G48175.1 | Symbols:  | FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: hypocotyl, male gametophyte, root; BEST Arabidopsis thaliana protein match is: Glycosyl hydrolase superfamily protein (TAIR:AT3G09260.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). | chr5:19539208-19539676 FORWARD LENGTH=115
  &gt;AT5G50920.1 | Symbols: CLPC, ATHSP93-V, HSP93-V, DCA1, CLPC1 | CLPC homologue 1 | chr5:20715710-20719800 REVERSE LENGTH=929
  </code></pre>
  
  <p>I would like to get something like</p>
  
  <pre><code>AT3G09260.1    2
  AT5G50920.1    2
  </code></pre>
  
  <p>I have tried</p>
  
  <pre><code>grep -f pattern.txt -c inputfile.txt
  4
  </code></pre>
  
  <p>but it only gives me the total number of matching lines (for all the patterns).
  I believe the question was already asked here but never solved  </p>
  
  <p><a href="https://stackoverflow.com/q/29494331/3257452">how to loop over pattern from a file with grep</a></p>
  
  <p>Thank you.</p>