Commit 01c9ce7a authored by Penom Nom's avatar Penom Nom
Browse files

split sff pre-treatment : shhhflows + trimseqs

parent 901cf3d9
......@@ -45,11 +45,26 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<input type="hidden" id="data_folder" value="{$data_folder}"/>
<input type="hidden" id="analysis_folder" value="{$data_folder|cat:$analyse.directory}"/>
<table class="table table-striped table-bordered dataTable analysis-result-table">
<thead>
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
{foreach from=$analyse_results_sorted key=sample item=sample_results}
{if $sample == "b"}
<p>There are {$sample_results["default"].ids_failed_trim_seqs} sequences deleted because of a problem with the barcode.</p>
{/if}
{if $sample == "lb"}
<p>There are {$sample_results["default"].ids_failed_trim_seqs} sequences deleted because of a wrong length and a problem with the barcode.</p>
{/if}
{if $sample == "l"}
<p>There are {$sample_results["default"].ids_failed_trim_seqs} sequences deleted because of a wrong length.</p>
{/if}
{/foreach}
<tr>
{if $analyse_results|@count > 1 }
{if $analyse_results|@count > 1}
{$analyse_results=$analyse_results|array_diff_key:(['b']|array_flip)}
{$analyse_results=$analyse_results|array_diff_key:(['lb']|array_flip)}
{$analyse_results=$analyse_results|array_diff_key:(['l']|array_flip)}
<th>Samples ({$analyse_results|@count})</th>
{/if}
<th>Number of sequences</th>
......@@ -57,17 +72,18 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</thead>
<tbody>
{assign var="nb_reads_begining" value=0}
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
{assign var="i" value=0}
{foreach from=$analyse_results_sorted key=sample item=sample_results}
<tr>
{if $analyse_results|@count > 1 }
<td id="sample_id_{$i}">{$sample|get_description:$descriptions}</td>
{/if}
{$nb_reads_begining=$nb_reads_begining+$sample_results["default"].nb_seq}
<td>{$sample_results["default"].nb_seq|number_format:0:' ':' '}</td>
</tr>
{$i = $i +1}
{if $sample != "b" and $sample !="lb" and $sample !="l"}
<tr>
{if $analyse_results|@count > 1 }
<td id="sample_id_{$i}">{$sample|get_description:$descriptions}</td>
{/if}
{$nb_reads_begining=$nb_reads_begining+$sample_results["default"].nb_seq}
<td>{$sample_results["default"].nb_seq|number_format:0:' ':' '}</td>
</tr>
{$i = $i +1}
{/if}
{/foreach}
</tbody>
<tfoot>
......
......@@ -92,7 +92,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{if $analyse_results|@count > 1 }
<td id="sample_id_{$i}">{$sample|get_description:$descriptions}</td>
{/if}
{$nb_reads_begining=$nb_reads_begining+$sample_results["default"].nb_seq_after_demultiplexage_after_demultiplexage}
{$nb_reads_begining=$nb_reads_begining+$sample_results["default"].nb_seq_after_demultiplexage}
{$primers_failed=$primers_failed+$sample_results["default"].f+$sample_results["default"].fl}
{$length_failed=$length_failed+$sample_results["default"].l}
{$homopolymers_failed=$homopolymers_failed+$sample_results["default"].h}
......
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