<div dir="ltr">Hi everyone,<div><br></div><div>I am trying to use MISO to assess the transcriptomes of cichlid fishes. I have run into</div><div>some problems while doing this and would appreciate your help:</div><div><br></div><div><b>1.</b>The <span style="color:rgb(255,255,255);font-family:Menlo;font-size:11px;background-color:rgb(0,0,0)">index_gff.py</span> generates the indexed annotations but it adds a chr in front of the</div><div>"LG" labels when it creates the indexes. So "LG1" is changes to "chrLG1" and so on. Should</div><div>I fix the names of these folders or let them be? Since in my BAM files and GFF files, the</div><div>label is "LG1".</div><div><br></div><div><b>2. </b>Also, when i try to generate the gff with consecutive exons using the following command:</div><div><br></div><div><p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">/export/bio/python/Python-2.7.5/bin/python /export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py --get-const-exons Oreochromis_niloticus.BROADON2.gff --min-exon-size 1000 --output-dir ./exons/</p></div><div><div><br></div><div>I get the following error:</div><div><p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">Getting constitutive exons...</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> - Input GFF: /nas2/pooja/pharyngeal_jaw_transcriptomes/raw_demultiplexed_bam/paper1/map2Onil/all_bam/alternative_splicing/Oreochromis_niloticus.BROADON2.gff</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> - Output dir: /nas2/pooja/pharyngeal_jaw_transcriptomes/raw_demultiplexed_bam/paper1/map2Onil/all_bam/alternative_splicing/exons</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> - Output format: gff</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> - Including only exons greater than or equal to 1000-bp</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">Constitutive exon retrieval took 86.17 seconds (2782 exons).</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">Outputting exons to file: /nas2/pooja/pharyngeal_jaw_transcriptomes/raw_demultiplexed_bam/paper1/map2Onil/all_bam/alternative_splicing/exons/Oreochromis_niloticus.BROADON2.min_1000.const_exons.gff</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">Traceback (most recent call last):</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> File "/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py", line 369, in <module></p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> main()</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> File "/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py", line 363, in main</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> min_size=options.min_exon_size)</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> File "/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py", line 314, in get_const_exons_by_gene</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> output_format=output_format)</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> File "/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py", line 103, in output_exons_to_file</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> gff_writer.write_recs(recs)</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> File "/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/gff_utils.py", line 888, in write_recs</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> self.write(rec)</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> File "/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/gff_utils.py", line 883, in write</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> self._record_writer(rec)</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> File "/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/gff_utils.py", line 918, in _write_rec_v3</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> fields = [_seqid_pat.sub(url_quote, rec.seqid),</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> File "/export/bio/python/Python-2.7.5/lib/python2.7/urllib.py", line 1280, in quote</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)"> if not s.rstrip(safe):</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">AttributeError: '_sre.SRE_Match' object has no attribute 'rstrip'</p></div><div><br></div><div>I am not sure what I am doing wrong since my gff file looks good (some lines pasted below).<br></div><div>I would appreciate if someone could tell me what I am doing wrong!</div><div><br></div><div><br></div><div>my GFF:</div><div><br></div><div><p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">##gff3-version3</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>gene<span class="" style="white-space:pre"> </span>5964<span class="" style="white-space:pre"> </span>9889<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.gene.LG1.1;Name=on.gene.LG1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>mRNA<span class="" style="white-space:pre"> </span>5964<span class="" style="white-space:pre"> </span>9889<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.1;Name=on.gene.LG1.1;Parent=on.gene.LG1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>5964<span class="" style="white-space:pre"> </span>6017<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.1.1;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>7911<span class="" style="white-space:pre"> </span>8060<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.1.2;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>8147<span class="" style="white-space:pre"> </span>8269<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.1.3;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>8386<span class="" style="white-space:pre"> </span>8584<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.1.4;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>8669<span class="" style="white-space:pre"> </span>8784<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.1.5;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>8980<span class="" style="white-space:pre"> </span>9034<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.1.6;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>9822<span class="" style="white-space:pre"> </span>9889<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.1.7;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>mRNA<span class="" style="white-space:pre"> </span>5964<span class="" style="white-space:pre"> </span>8290<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.2;Name=on.gene.LG1.1;Parent=on.gene.LG1.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>5964<span class="" style="white-space:pre"> </span>6017<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.2.1;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.2</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>7911<span class="" style="white-space:pre"> </span>8060<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.2.2;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.2</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>8147<span class="" style="white-space:pre"> </span>8290<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>+<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.1.2.3;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.2</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>gene<span class="" style="white-space:pre"> </span>13041<span class="" style="white-space:pre"> </span>54863<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.gene.LG1.2;Name=on.gene.LG1.2</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>mRNA<span class="" style="white-space:pre"> </span>16786<span class="" style="white-space:pre"> </span>54863<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.2.1;Name=on.gene.LG1.2;Parent=on.gene.LG1.2</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>16786<span class="" style="white-space:pre"> </span>16986<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.2.1.8;Name=on.gene.LG1.2;Parent=on.mrna.LG1.2.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>17288<span class="" style="white-space:pre"> </span>17392<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.2.1.7;Name=on.gene.LG1.2;Parent=on.mrna.LG1.2.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>17496<span class="" style="white-space:pre"> </span>17612<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.2.1.6;Name=on.gene.LG1.2;Parent=on.mrna.LG1.2.1</p>
<p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(255,255,255);background-color:rgb(0,0,0)">LG1<span class="" style="white-space:pre"> </span>protein_coding<span class="" style="white-space:pre"> </span>exon<span class="" style="white-space:pre"> </span>17785<span class="" style="white-space:pre"> </span>17949<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>ID=on.mrna.LG1.2.1.5;Name=on.gene.LG1.2;Parent=on.mrna.LG1.2.1</p></div><div><br></div><div><br></div><div><br></div><div><br></div><div>Best regards,</div><div><br></div><div>Pooja Singh</div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div><span><font color="#333333"><b>PhD student</b></font></span></div><div><span><font color="#333333"><b>Institute of Zoology</b></font></span></div><div><span><font color="#333333"><b>Universitätplatz 2</b></font></span></div><div><span><font color="#333333"><b>University of Graz</b></font></span></div><div><span><font color="#333333"><b>Graz 8010</b></font></span></div><div><span><font color="#333333"><b>Austria<br></b></font>
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