<commit_before><p>Each program should</p>
<ul>
  <li>read all of a redirected <a href="http://en.wikipedia.org/wiki/Fasta_format">FASTA format</a> file from stdin</li>
  <li>define a collection of simple regex patterns,
   representing a 8-mer and it's reverse complement (with a wildcard in one position), 
   and count matches in the redirected file
  </li>
  <li>write the regex pattern and count</li>
</ul>


<p>We use FASTA files generated by the <a href="benchmark.php?test=fasta&amp;lang=all&amp;sort=<?=$Sort;?>">fasta benchmark</a> as input for this benchmark. Note: the file may include both lowercase and uppercase codes.</p>

<p>Correct output for this 100KB <a href="iofile.php?test=<?=$SelectedTest;?>&amp;lang=<?=$SelectedLang;?>&amp;sort=<?=$Sort;?>&amp;file=input">input file</a> (generated with the fasta program N = 10000), is</p>
<pre>
(agggtaaa)|(tttaccct) 0
([cgt]gggtaaa)|(tttaccc[acg]) 3
(a[act]ggtaaa)|(tttacc[agt]t) 8
(ag[act]gtaaa)|(tttac[agt]ct) 8
(agg[act]taaa)|(ttta[agt]cct) 7
(aggg[acg]aaa)|(ttt[cgt]ccct) 3
(agggt[cgt]aa)|(tt[acg]accct) 4
(agggta[cgt]a)|(t[acg]taccct) 3
(agggtaa[cgt])|([acg]ttaccct) 5
</pre>
<br />

<p></p>
<commit_msg>*** empty log message ***<commit_after><p>Each program should</p>
<ul>
  <li>read all of a redirected <a href="http://en.wikipedia.org/wiki/Fasta_format">FASTA format</a> file from stdin</li>
  <li>define a collection of simple regex patterns,
   representing a 8-mer and it's reverse complement (with a wildcard in one position), 
   and count matches in the redirected file
  </li>
  <li>write the regex pattern and count</li>
</ul>


<p>We use FASTA files generated by the <a href="benchmark.php?test=fasta&amp;lang=all&amp;sort=<?=$Sort;?>">fasta benchmark</a> as input for this benchmark. Note: the file may include both lowercase and uppercase codes.</p>

<p>Correct output for this 100KB <a href="iofile.php?test=<?=$SelectedTest;?>&amp;lang=<?=$SelectedLang;?>&amp;sort=<?=$Sort;?>&amp;file=input">input file</a> (generated with the fasta program N = 10000), is</p>
<pre>
agggtaaa|(tttaccct) 0
[cgt]gggtaaa|tttaccc[acg] 3
a[act]ggtaaa|tttacc[agt]t 8
ag[act]gtaaa|tttac[agt]ct 8
agg[act]taaa|ttta[agt]cct 7
aggg[acg]aaa|ttt[cgt]ccct 3
agggt[cgt]aa|tt[acg]accct 4
agggta[cgt]a|t[acg]taccct 3
agggtaa[cgt]|[acg]ttaccct 5
</pre>
<br />

<p></p>

{'fraction_non_alphanumeric': 0.17844827586206896, 'fraction_numerical': 0.015517241379310345, 'mean_word_length': 6.230529595015576, 'pattern_counts': {'":': 0, '<': 61, '<?xml version=': 0, '>': 61, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '351631', 'n_tokens_mistral': 993, 'n_tokens_neox': 932, 'n_words': 230}