Dear Galaxy team / user mailing list,<br><br>my question is with respect to command line usage, not about interactive / web-based Galaxy usage. Regarding the publication [1], section &quot;2.3 Stitchers&quot;.<br><br>I want to use the stitcher to extract a given region from MAF files, stitch it together and convert it to FASTA.<br>
<br>I downloaded and installed Galaxy according to the instructions from <a href="http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy">http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy</a><br><br>I believe the actual stitcher is &quot;interval_maf_to_merged_fasta.py&quot; in the /tools/maf directory (not clear from the paper or docs but I belive this is the tool that implements this functionality).<br>
<br>How can I actually extract, stitch, convert with interval_maf_to_merged_fasta.py?<br><br>I have difficulties figuring all necessary command line parameters out by reading the source code.<br><br>F.e. here I tried to get the stiched FASTA conversion for a region defined in &quot;foo.bed&quot; out of &quot;chr1.maf&quot;:<br>
<br><span style="font-family:courier new,monospace">$ python ./tools/maf/interval_maf_to_merged_fasta.py -G -i ../foo.bed -m ../chr1.maf -d hg18 -o stdout</span><br style="font-family:courier new,monospace"><span style="font-family:courier new,monospace">Traceback (most recent call last):</span><br style="font-family:courier new,monospace">
<span style="font-family:courier new,monospace">  File &quot;./tools/maf/interval_maf_to_merged_fasta.py&quot;, line 196, in &lt;module&gt;</span><br style="font-family:courier new,monospace"><span style="font-family:courier new,monospace">    if __name__ == &quot;__main__&quot;: __main__()</span><br style="font-family:courier new,monospace">
<span style="font-family:courier new,monospace">  File &quot;./tools/maf/interval_maf_to_merged_fasta.py&quot;, line 107, in __main__</span><br style="font-family:courier new,monospace"><span style="font-family:courier new,monospace">    if options.mafSourceType.lower() in [&quot;cached&quot;]:</span><br style="font-family:courier new,monospace">
<span style="font-family:courier new,monospace">AttributeError: &#39;NoneType&#39; object has no attribute &#39;lower&#39;</span><br style="font-family:courier new,monospace"><br>Is it necessary to index the MAF files first somehow? Do I have to set the type of MAF file, and to what?<br>
<br>Would be great if someone could give a short overview how to stitch MAF files command-line based.<br><br>Thank you!<br><br>Anton<br><br><span>References<br>[1] Blankenberg, D., Taylor, J.,
  Nekrutenko, A. &amp; Galaxy Team.
 Making whole genome multiple alignments usable for
  biologists.
 <em>Bioinformatics (Oxford, England)</em>
  <b>27</b>, 2426-2428
  (2011)<br><br><br></span>