<div dir="ltr"><span style="font-size:12.8px">Dear All,</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">I'm new with parsing gff files while I'm trying to parse the gff files I found that the start position of the gene is </span><b style="font-size:12.8px">8774510 instead of </b><b style="font-size:12.8px">8774511 (in the original files)</b><span style="font-size:12.8px">, Could any one explain that for me:</span><div style="font-size:12.8px"><br>> grep "gene:Bra000001" Brassica_rapa.IVFCAASv1.34.chr<wbr>.gff3<br><br>>A03 brad gene <b>8774511</b> <b>8777095</b> . + . ID=gene:Bra000001;biotype=prot<wbr>ein_coding;description=AT2G374<wbr>40 (E%3D7e-179) | endonuclease/exonuclease/phosp<wbr>hatase family protein ;gene_id=Bra000001;logic_name=<wbr>glean<br>A03 brad mRNA 8774511 8777095 . + . ID=transcript:Bra000001.1;Pare<wbr>nt=gene:Bra000001;biotype=prot<wbr>ein_coding;transcript_id=Bra00<wbr>0001.1<br><br><br>after using the following script <br>=============================<br><div>from BCBio import GFF</div><div>in_file = "chr.gff3"</div><div>limits = dict(gff_type = ["gene","mRNA","exon"])</div><div>gff_handle = open(in_file)</div><div>for rec in GFF.parse(gff_handle,target_li<wbr>nes=1000,limit_info=limits):</div><div>    for gene_feature in rec.features:</div><div><span class="gmail-m_8270932553248671089m_8400940231785708940gmail-Apple-tab-span" style="white-space:pre-wrap">     </span>if <a href="http://gene_feature.id/" target="_blank">gene_feature.id</a> == 'gene:Bra000001':</div><div><span class="gmail-m_8270932553248671089m_8400940231785708940gmail-Apple-tab-span" style="white-space:pre-wrap">           </span>print(<a href="http://gene_feature.id/" target="_blank">gene_feature.id</a>,gene_fea<wbr>ture.location)</div><div>============================</div><div>The result in the following, tell us that the start position for the same gene is <b>8774510 instead of </b><b>8774511</b></div><div>>('gene:Bra000001', FeatureLocation(ExactPosition(<b><wbr>8774510</b>), ExactPosition(<b>8777095</b>), strand=1)</div></div></div>