anchor.diff:      <h5>Example</h5>
       <pre>
   <b>$</b> cat input.txt
  -AALTER
  +ISVAQGASK
   OMGWTFBBQ
   MDGTEYIIVK
   <b>$</b> unipept pept2prot <b>--input</b> input.txt
  -peptide,taxon_id,taxon_name,taxon_rank
  -AALTER,1,root,no rank
  -MDGTEYIIVK,1263,Ruminococcus,genus</pre>
  +peptide,uniprot_id,protein_name,taxon_id
  +ISVAQGASK,Q9Y6R7,IgGFc-binding protein,9606
  +ISVAQGASK,A0A087WXI2,IgGFc-binding protein,9606
  +MDGTEYIIVK,C6JD41,10 kDa chaperonin,457412</pre>
       <h3 id='#param-output'><samp>--output</samp> / <samp>-o</samp> <small>Specify an output file</small></h3>
       <p>
         By default, the unipept commands write their output to <i>standard output</i>. Using the optional <code>--output</code> option allows you to specify a file to write the output to. If the file already exists, the output will be appended; if it doesn't, a new file will be created.
       </p>
       <h5>Example</h5>
       <pre>
  -<b>$</b> unipept pept2prot <b>--output</b> output.txt AALTER
  +<b>$</b> unipept pept2prot <b>--output</b> output.txt ISVAQGASK MDGTEYIIVK
   <b>$</b> cat output.txt
  -peptide,taxon_id,taxon_name,taxon_rank
  -AALTER,1,root,no rank</pre>
  +peptide,uniprot_id,protein_name,taxon_id
  +ISVAQGASK,Q9Y6R7,IgGFc-binding protein,9606
  +ISVAQGASK,A0A087WXI2,IgGFc-binding protein,9606
  +MDGTEYIIVK,C6JD41,10 kDa chaperonin,457412</pre>
       <h3 id='#param-input'><samp>--select</samp> / <samp>-s</samp> <small>Specify the output fields</small></h3>
       <p>
         By default, the Unipept <span class='initialism'>CLI</span> commands output all information fields received from the Unipept server. The <code>--select</code> option allows you to control which fields are returned. A list of fields can be specified by a comma-separated list, or by using multiple <code>--select</code> options. A <samp>*</samp> can be used as a wildcard for field names. For example, <code>--select peptide,taxon*</code> will return the peptide field and all fields starting with <i>taxon</i>.
       </p>
       <h5>Example</h5>
       <pre>
  -<b>$</b> unipept pept2prot <b>--select</b> peptide,taxon_id AALTER
  -peptide,taxon_id
  -AALTER,1
  -<b>$</b> unipept pept2prot <b>--select</b> peptide <b>--select</b> *name AALTER
  -peptide,taxon_name
  -AALTER,root</pre>
  +<b>$</b> unipept pept2prot <b>--select</b> peptide,uniprot_id MDGTEYIIVK
  +peptide,uniprot_id
  +MDGTEYIIVK,C6JD41
  +<b>$</b> unipept pept2prot <b>--select</b> peptide <b>--select</b> *id MDGTEYIIVK
  +peptide,uniprot_id,taxon_id
  +MDGTEYIIVK,C6JD41,457412</pre>
       <h3 id='#param-format'><samp>--format</samp> / <samp>-f</samp> <small>Specify the output format</small></h3>
       <p>
         By default, the Unipept <span class='initialism'>CLI</span> commands return their output in <samp>csv</samp> format. The <code>--format</code> option allows you to select another format. Supported formats are <samp>csv</samp>, <samp>json</samp>, and <samp>xml</samp>.
       </p>
       <h5>Example</h5>
       <pre>
  -<b>$</b> unipept pept2prot <b>--format</b> json AALTER MDGTEYIIVK
  -[{"peptide":"AALTER","taxon_id":1,"taxon_name":"root","taxon_rank":"no rank"},{"peptide":"MDGTEYIIVK","taxon_id":1263,"taxon_name":"Ruminococcus","taxon_rank":"genus"}]
  -<b>$</b> unipept pept2prot <b>--format</b> xml AALTER MDGTEYIIVK
  -&lt;results&gt;&lt;result&gt;&lt;peptide&gt;AALTER&lt;/peptide&gt;&lt;taxon_id&gt;1&lt;/taxon_id&gt;&lt;taxon_name&gt;root&lt;/taxon_name&gt;&lt;taxon_rank&gt;no rank&lt;/taxon_rank&gt;&lt;/result&gt;&lt;result&gt;&lt;peptide&gt;MDGTEYIIVK&lt;/peptide&gt;&lt;taxon_id&gt;1263&lt;/taxon_id&gt;&lt;taxon_name&gt;Ruminococcus&lt;/taxon_name&gt;&lt;taxon_rank&gt;genus&lt;/taxon_rank&gt;&lt;/result&gt;&lt;/results&gt;</pre>
  +<b>$</b> unipept pept2prot <b>--format</b> json ISVAQGASK MDGTEYIIVK
  +[{"peptide":"ISVAQGASK","uniprot_id":"Q9Y6R7","protein_name":"IgGFc-binding protein","taxon_id":9606},{"peptide":"ISVAQGASK","uniprot_id":"A0A087WXI2","protein_name":"IgGFc-binding protein","taxon_id":9606},{"peptide":"MDGTEYIIVK","uniprot_id":"C6JD41","protein_name":"10 kDa chaperonin","taxon_id":457412}]
  +<b>$</b> unipept pept2prot <b>--format</b> xml ISVAQGASK MDGTEYIIVK
  +&lt;results&gt;&lt;result&gt;&lt;peptide&gt;ISVAQGASK&lt;/peptide&gt;&lt;uniprot_id&gt;Q9Y6R7&lt;/uniprot_id&gt;&lt;protein_name&gt;IgGFc-binding protein&lt;/protein_name&gt;&lt;taxon_id&gt;9606&lt;/taxon_id&gt;&lt;/result&gt;&lt;result&gt;&lt;peptide&gt;ISVAQGASK&lt;/peptide&gt;&lt;uniprot_id&gt;A0A087WXI2&lt;/uniprot_id&gt;&lt;protein_name&gt;IgGFc-binding protein&lt;/protein_name&gt;&lt;taxon_id&gt;9606&lt;/taxon_id&gt;&lt;/result&gt;&lt;result&gt;&lt;peptide&gt;MDGTEYIIVK&lt;/peptide&gt;&lt;uniprot_id&gt;C6JD41&lt;/uniprot_id&gt;&lt;protein_name&gt;10 kDa chaperonin&lt;/protein_name&gt;&lt;taxon_id&gt;457412&lt;/taxon_id&gt;&lt;/result&gt;&lt;/results&gt;</pre>
       <h3 id='#param-all'><samp>--all</samp> / <samp>-a</samp> <small>Request additional information</small></h3>
       <p>
  -      By default, the Unipept <span class='initialism'>CLI</span> commands only request basic information from the Unipept server. By using the <code>--all</code> flag, you can request additional information fields such as the lineage of the returned taxa. You can use the <code>--select</code> option to select which fields are included in the output.
  +      By default, the Unipept <span class='initialism'>CLI</span> commands only request basic information from the Unipept server. By using the <code>--all</code> flag, you can request additional information fields such as cross references of the returned UniProt entries. You can use the <code>--select</code> option to select which fields are included in the output.
       </p>
       <div class="apidocs-callout apidocs-callout-warning">
         <h4>Performance penalty</h4>
  
positive.code:     </div>
      <h5>Example</h5>
      <pre>
  <b>$</b> unipept pept2prot <b>--all</b> --select peptide,taxon_id,order* MDGTEYIIVK
  peptide,taxon_id,order_id,order_name
  MDGTEYIIVK,1263,186802,Clostridiales</pre>
      <h3><samp>--help</samp> / <samp>-h</samp> <small>Display help</small></h3>
      <p>
        This flag displays the help.
  
negative.code:       If the <code>--equate</code> flag is set, isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records. This is similar to checking the <i>Equate I and L?</i> checkbox when performing a search in the Unipept web interface.
      </p>
      <pre>
  <b>$</b> unipept pept2prot FEALLGDGSQYGLHLQYK
  peptide,uniprot_id,protein_name,taxon_id
  FEALLGDGSQYGLHLQYK,D1PLT2,Glucose-1-phosphate thymidylyltransferase,411471
  FEALLGDGSQYGLHLQYK,K1TWG3,"Glucose-1-phosphate thymidylyltransferase, long form",408170
  <b>$</b> unipept pept2prot <b>--equate</b> FEALLGDGSQYGLHLQYK
  peptide,uniprot_id,protein_name,taxon_id
  FEALLGDGSQYGLHLQYK,D4K7A9,Glucose-1-phosphate thymidylyltransferase,657322
  FEALLGDGSQYGLHLQYK,D4K112,Glucose-1-phosphate thymidylyltransferase,718252
  FEALLGDGSQYGLHLQYK,D1PLT2,Glucose-1-phosphate thymidylyltransferase,411471
  FEALLGDGSQYGLHLQYK,A8SH27,Glucose-1-phosphate thymidylyltransferase,411485
  FEALLGDGSQYGLHLQYK,K1TWG3,"Glucose-1-phosphate thymidylyltransferase, long form",408170
  FEALLGDGSQYGLHLQYK,E2ZLF5,Glucose-1-phosphate thymidylyltransferase,748224
  FEALLGDGSQYGLHLQYK,R6Q2J6,Glucose-1-phosphate thymidylyltransferase,1262898
  FEALLGDGSQYGLHLQYK,C7HAW8,Glucose-1-phosphate thymidylyltransferase,411483</pre>
      <h3><samp>--input</samp> / <samp>-i</samp> <small>Specify an input file</small></h3>
      <p>
        All Unipept <span class='initialism'>CLI</span> commands can process input from 3 sources: command line arguments, a file, or <i>standard input</i>. The optional <code>--input</code> option allows you to specify an input file. The file should contain a single peptide per line.
  