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Commit 4483ba49 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

output path modified

parent 0c28bcd5

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.
...@@ -16,7 +16,7 @@ def transyt(processingPath, resultsPath): ...@@ -16,7 +16,7 @@ def transyt(processingPath, resultsPath):
logging.basicConfig(filename=logPath, level=logging.DEBUG, format='%(asctime)s: %(levelname)s: >>>%(message)s') logging.basicConfig(filename=logPath, level=logging.DEBUG, format='%(asctime)s: %(levelname)s: >>>%(message)s')
output_path = resultsPath + "/" # + "/results_biocoiso.json" output_path = resultsPath + "/"
logging.info("The results path is " + output_path) logging.info("The results path is " + output_path)
runTransyt(output_path, processingPath+"/" ) runTransyt(output_path, processingPath+"/" )
...@@ -50,9 +50,9 @@ def runTransyt(output_path, processingPath): ...@@ -50,9 +50,9 @@ def runTransyt(output_path, processingPath):
else: else:
logging.info("TranSyT run well and the zip file and the md5 file is going to be created.") logging.info("TranSyT run well and the zip file and the md5 file is going to be created.")
if os.path.exists(processingPath): #if os.path.exists(processingPath):
shutil.rmtree(processingPath) # shutil.rmtree(processingPath)
logging.info("The processing directory was removed succefully.") # logging.info("The processing directory was removed succefully.")
def get_all_file_paths(directory): def get_all_file_paths(directory):
......
...@@ -99,7 +99,7 @@ def display_msg(): ...@@ -99,7 +99,7 @@ def display_msg():
return jsonify({"result": "Time out"}), 408 return jsonify({"result": "Time out"}), 408
if "processComplete" in files: if "processComplete" in files:
return send_file(RESULTS_PATH + "results.zip", as_attachment=True, return send_file(SUBMISSIONS_PATH + "/results.zip", as_attachment=True,
attachment_filename='results.zip'), 200 attachment_filename='results.zip'), 200
return jsonify({"result": "running"}), 202 return jsonify({"result": "running"}), 202
......
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<div class="next-level"><a href="/search/result.php?tc=1.A.100.3">View Proteins belonging to: <span style="color:maroon;">The Rhabdoviridae Putative Viroporin, U5 (RV-U5) Family</span></a></div>
<!-- <div class="title">1.A.100: The Rhabdoviridae Putative Viroporin, U5 (RV-U5) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.100 The Rhabdoviridae Putative Viroporin, U5 (RV-U5) Family&nbsp;</strong></p>
<p>Viruses belonging to the family Rhabdoviridae infect a variety of
different hosts including insects, vertebrates and plants. There are over 200 rhabdoviruses isolated
around the world.&nbsp; The complete genome sequence
and predicted transcription strategy of Wongabel <span class='highlight'>virus</span> (WONV), a&nbsp; rhabdovirus isolated from biting
midges (<em>Culicoides austropalpalis</em>) is available. The 13,196 nucleotide genome encodes five typical
rhabdovirus genes N, P, M, G and L, plus three genes located between the P and M genes (U1, U2, U3) and
two overlapping the N and G genes (U4, U5). The U5 gene product has characteristics
typical of viroporins with structural similarities with the
alpha-1 <span class='highlight'>protein</span> (putative viroporin) of viruses in the genus Ephemerovirus, and similarity with the <span class='highlight'>avian</span>-associated Flanders <span class='highlight'>virus</span> has been noted (<a class="reflink" href="/search/result.php?tc=1.A.100#ref34544547">Gubala <em>et al.</em> 2008</a>).&nbsp;</p>
<p>Viroporins are viral ion channel proteins usually with 50-120 amino acids.&nbsp; They play important roles in regulating virus replication, including virus entry, assembly and release. They may also modulate the electrochemical
balance in subcellular compartments of the host cells. <a class="reflink" href="/search/result.php?tc=1.A.100#ref34550060">Wang <em>et al.</em> 2011 </a>summarized advances concerning&nbsp;
viroporins, including PBCV-1 KcV, influenza M2, HIV-1 Vpu, HCV p7,
picornavirus 2B, and the coronavirus E and 3a viroporins with emphasis on their function s
and mechanisms.</p></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.100.3">View Proteins belonging to: <span style="color:maroon;">The Rhabdoviridae Putative Viroporin, U5 (RV-U5) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.100 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34544547"></A>Gubala, A.J., D.F. Proll, R.T. Barnard, C.J. Cowled, S.G. Crameri, A.D. Hyatt, and D.B. Boyle. (2008). Genomic characterisation of Wongabel virus reveals novel genes within the Rhabdoviridae. Virology 376: 13-23. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=18436275" target="_window">18436275</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34550060"></A>Wang, K., S. Xie, and B. Sun. (2011). Viral proteins function as ion channels. Biochim. Biophys. Acta. 1808: 510-515. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=20478263" target="_window">20478263</A></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.101.8">View Proteins belonging to: <span style="color:maroon;">The Peroxisomal Pore-forming Pex11 (Pex11) Family</span></a></div>
<!-- <div class="title">1.A.101: The Peroxisomal Pore-forming Pex11 (Pex11) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.101 The Peroxisomal Pore-forming Pex11 (Pex11) Family</strong></p>
<p>More than thirty Pex proteins are known to participate in the biogenesis of peroxisomes, oxidative organelles involved in lipid and ROS metabolism. Pex11 homologues are constituents of the Pexoxisomal Protein Importer (PPI) Family (TC# 3.A.20). They play roles, direct or indirect, in division and proliferation of peroxisomes (<a class="reflink" href="/search/result.php?tc=1.A.101#ref34544772">Schrader <em>et al.</em> 1998</a>).&nbsp;<a class="reflink" href="/search/result.php?tc=1.A.101#ref34544773">Mindthoff <em>et al.</em> 2015</a> showed that yeast Pex11 is a
pore-forming protein, possibly sharing significant sequence similarity with TRPM cation-selective channels. The Pex11
channel is moderately cation-selective
(PK<sup>+</sup>/PCl<sup>-</sup>=1.85) and resistant to voltage-dependent closing. The estimated size of the channel's pore
(r~0.6nm) supports the notion that Pex11 conducts solutes with molecular mass below 300-400 Da, and the channel's selectivity filter was localized. Overproduction of Pex11 resulted in acceleration of
fatty acids beta-oxidation in intact cells but not in the corresponding lysates. Beta-oxidation in cells was affected by expression of the Pex11 protein carrying point mutations in the selectivity
filter. These data suggested that the Pex11-dependent transmembrane traffic of metabolites may be a
rate-limiting step in the beta-oxidation of fatty acids. This conclusion was corroborated by
analysis of the rate of beta-oxidation in yeast strains expressing Pex11 with mutations mimicking
constitutively phosphorylated (S165D, S167D) or unphosphorylated (S165A, S167A) protein. The results
suggest that phosphorylation of Pex11 is a mechanism that can control the peroxisomal beta-oxidation
rate.&nbsp; Pex11 is thus a non-selective channel responsible
for transfer of metabolites across peroxisomal membrane.(<a class="reflink" href="/search/result.php?tc=1.A.101#ref34544773">Mindthoff <em>et al.</em> 2015</a>).</p></div>
<div class="result-superfam">This family belongs to the:<a href="/superfamily.php?id=76"> Peroxisomal Peroxin (Pex)11/25/27 (Pex11/25/27) Superfamily</a>.</div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.101.8">View Proteins belonging to: <span style="color:maroon;">The Peroxisomal Pore-forming Pex11 (Pex11) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.101 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34545748"></A>Jaiteh, M., A. Taly, and J. Hénin. (2016). Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors. PLoS One 11: e0151934. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26986966" target="_window">26986966</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34544773"></A>Mindthoff S., Grunau S., Steinfort LL., Girzalsky W., Hiltunen JK., Erdmann R. and Antonenkov VD. (2015). Peroxisomal Pex11 is a pore-forming protein homologous to TRPM channels. Biochim Biophys Acta. 1863(2):271-283. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26597702" target="_window">26597702</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34544772"></A>Schrader, M., B.E. Reuber, J.C. Morrell, G. Jimenez-Sanchez, C. Obie, T.A. Stroh, D. Valle, T.A. Schroer, and S.J. Gould. (1998). Expression of PEX11beta mediates peroxisome proliferation in the absence of extracellular stimuli. J. Biol. Chem. 273: 29607-29614. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=9792670" target="_window">9792670</A></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.102.1">View Proteins belonging to: <span style="color:maroon;">The Influenza A viroporin PB1-F2 (PB1-F2) Family</span></a></div>
<!-- <div class="title">1.A.102: The Influenza A viroporin PB1-F2 (PB1-F2) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.102 The Influenza A viroporin PB1-F2 (PB1-F2) Family</strong></p>
<p>The PB1-F2 protein of 90 aas, and possibly a weakly hydrophobic C-terminal TMS, exhibits viroporin activity, transporting monovalent cations and Ca<sup>2+ </sup>(<a class="reflink" href="/search/result.php?tc=1.A.102#ref34545079">Hyser and Estes 2015</a>).&nbsp;</p></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.102.1">View Proteins belonging to: <span style="color:maroon;">The Influenza A viroporin PB1-F2 (PB1-F2) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.102 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34545080"></A>Hyser, J.M. and M.K. Estes. (2015). Pathophysiological Consequences of Calcium-Conducting Viroporins. Annu Rev Virol 2: 473-496. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26958925" target="_window">26958925</A></div>
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