Merge pull request bjtully#47 from bjtully/underdevelopment

Updating coding for V1.2

KEGGDecoder/KEGG_decoder.py

@@ -1,7 +1,12 @@
 #!/usr/bin/python
 
 '''
-KEGG-decoder.py V.1.1
+KEGG-decoder.py V.1.2
+V.1.2
+Added several new pathways including PET degradation, carbon storage,
+related to starch/gylcogen & polyhydroxybutyrate, and posphate storage,
+related to the reversible polyphosphate reaction. Part of summer research
+with Sheyla Aviles.
 V.1.1
 Correcting typos identified by Chris Neely. Adding more complete
 pathways components for amino acid biosynthesis identified by
@@ -1357,6 +1362,78 @@ def amino_acids(ko_match):
 
 	return out_data
 
+def plastic(ko_match):
+	out_data = {"PET degradation": 0}
+	#poly(ethylene terephthalate) hydrolase
+	#mono(ethylene terephthalate) hydrolase
+	#1,2-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase
+	petdeg = ["K21104", "K21105", "K18076"]
+	for i in petdeg:
+		if i in ko_match:
+			out_data["PET degradation"] += 0.25
+	#terephthalate 1,2-dioxygenase oxygenase
+	#two possible versions
+	if ("K18077" in ko_match) or ("K18074" in ko_match and "K18075" in ko_match):
+		out_data["PET degradation"] += 0.25
+
+	return out_data
+
+def carbon_storage(ko_match):
+    out_data = {'starch/glycogen synthesis': 0, 'starch/glycogen degradation': 0, 'polyhydroxybutyrate synthesis': 0}
+    # starch synthesis
+    carbonsto = ["K00703", "K00975"]
+    for i in carbonsto:
+        if i in ko_match:
+            out_data["starch/glycogen synthesis"] += 0.33
+
+    if ('K00700' in ko_match) or ('K16149' in ko_match):
+        out_data['starch/glycogen synthesis'] += 0.33
+    #starch > D-glucose
+		#K21574	susB; glucan 1,4-alpha-glucosidase
+    if ('K21574' in ko_match):
+        out_data['starch/glycogen degradation'] = 1
+    #starch > cyclodextrin
+    #K00701	cgt; cyclomaltodextrin glucanotransferase
+    if ('K00701' in ko_match):
+        out_data['starch/glycogen degradation'] = 1
+    #starch > maltodextrin
+    #K01214	treX; isoamylase
+    if ('K01214' in ko_match):
+        out_data['starch/glycogen degradation'] = 1
+    #starch > glucose-6P
+    if ('K00688' in ko_match) or ('K16153' in ko_match) or ('K00705' in ko_match) or ('K22451' in ko_match) or ('K02438' in ko_match) or ('K01200' in ko_match):
+        out_data['starch/glycogen degradation'] = 1
+    #starch > dextrin
+    #alpha-amlyase
+    if ('K01176' in ko_match) or ('K05343' in ko_match):
+        out_data['starch/glycogen degradation'] = 1
+    #beta-amlyase
+    if 'K01177' in ko_match:
+        out_data['starch/glycogen degradation'] = 1
+    #maltogenic alpha-amylase
+    if ('K05992' in ko_match) or ('K01208' in ko_match):
+        out_data['starch/glycogen degradation'] = 1
+    if ('K00023' in ko_match):
+        out_data['polyhydroxybutyrate synthesis'] += 0.5
+    phb = ['K00626', 'K03821', 'K22881']
+    for i in phb:
+        if i in ko_match:
+            out_data['polyhydroxybutyrate synthesis'] += 0.167
+
+    return out_data
+
+
+def phosphate_storage(ko_match):
+    out_data = {'bidirectional polyphosphate': 0}
+
+    if ('K00937' in ko_match) or ('K22468' in ko_match):
+        out_data['bidirectional polyphosphate'] += 0.5
+    if ('K01507' in ko_match) or ('K15986' in ko_match) or ('K06019' in ko_match):
+        out_data['bidirectional polyphosphate'] += 0.5
+
+    return out_data
+
+
 def default_viz(genome_df, outfile_name):
 	import seaborn as sns
 	import matplotlib.pyplot as plt
@@ -1485,7 +1562,9 @@ def main():
 	'threonine', 'asparagine', 'glutamine', 'cysteine',
 	'glycine', 'proline', 'alanine', 'valine', 
 	'methionine', 'phenylalanine', 'isoleucine', 'leucine',
-	'tryptophan', 'tyrosine', 'aspartate', 'glutamate']
+	'tryptophan', 'tyrosine', 'aspartate', 'glutamate', 'PET degradation',
+	'starch/glycogen synthesis', 'starch/glycogen degradation', 'polyhydroxybutyrate synthesis',
+	'bidirectional polyphosphate']
 
 
 	filehandle = str(arg_dict['output'])
@@ -1530,6 +1609,9 @@ def main():
 		pathway_data.update(arsenic(genome_data[k]))
 		pathway_data.update(metal_transport(genome_data[k]))
 		pathway_data.update(amino_acids(genome_data[k]))
+		pathway_data.update(plastic(genome_data[k]))
+		pathway_data.update(carbon_storage(genome_data[k]))
+		pathway_data.update(phosphate_storage(genome_data[k]))
 	#    print k, pathway_data
 
 		out_string = str(k)+"\t"
@@ -1562,14 +1644,17 @@ def main():
 
 	if arg_dict['vizoption'] == 'static':
 		from .KEGG_clustering import hClust_euclidean
+		#from KEGG_clustering import hClust_euclidean
 		if len(genome.index) >= 2 and not rearrange:
 			genome = hClust_euclidean(genome)
 		default_viz(genome, os.path.splitext(filehandle)[0] + ".svg")
 	if arg_dict['vizoption'] == 'interactive':
 		from .Plotly_viz import plotly_viz
+		#from Plotly_viz import plotly_viz
 		plotly_viz(genome, os.path.splitext(filehandle)[0] + ".html")
 	if arg_dict['vizoption'] == 'tanglegram':
 		from .MakeTanglegram import make_tanglegram
+		#from MakeTanglegram import make_tanglegram
 		if len(genome.index) >= 3:
 			make_tanglegram(genome, str(arg_dict['newick']), os.path.splitext(filehandle)[0] + ".tanglegram.svg", int(arg_dict["tangleopt"]))
 		else:

KEGGDecoder/KOALA_definitions.txt

@@ -1,4 +1,9 @@
 
+V.1.2
+Added several new pathways including PET degradation, carbon storage,
+related to starch/gylcogen & polyhydroxybutyrate, and posphate storage,
+related to the reversible polyphosphate reaction. Part of summer research
+with Sheyla Aviles.
 V.1.1
 Correcting typos identified by Chris Neely. Adding more complete
 pathways components for amino acid biosynthesis identified by
@@ -653,6 +658,35 @@ asparagine synthase (glutamine-hydrolysing)	asparagine - polar uncharged side ch
 	K00811	ASP5; OR K00812 aspB; K00813 aspC; K11358 yhdR; K14454 GOT1; K14455 GOT2 aspartate aminotransferase	glutamate - negative charge
 
 
-
-
+Polyethylene terephthalate degradation
+	K21104	poly(ethylene terephthalate) hydrolase
+	K21105	mono(ethylene terephthalate) hydrolase
+	K18074	tphA2; terephthalate 1,2-dioxygenase oxygenase component alpha subunit AND K18075 tphA3; terephthalate 1,2-dioxygenase oxygenase component beta subunit OR K18077	tphA1; terephthalate 1,2-dioxygenase reductase component
+	K18076	tphB; 1,2-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase
+
+Storage carbon (starch/glycogen) and phosphorous (polyphosphate)
+	STARCH Synthesis
+	K00703	glgA; starch synthase
+	K00975	glgC; glucose-1-phosphate adenylyltransferase
+	K00700	glgB; 1,4-alpha-glucan branching enzyme OR K16149 1,4-alpha-glucan branching enzyme
+	STARCH Degradation -- any pathway that converts glycogen will be included. Only recording 1 instance of transformation.
+	starch > glucose-6P
+		K00688	glgP; glycogen phosphorylase OR K16153 glycogen phosphorylase/synthase OR K00705 malQ; 4-alpha-glucanotransferase OR K22451 jgt; 4-alpha-glucanotransferase OR K02438 glgX; glycogen debranching enzyme OR K01200 pulA; pullulanase
+	starch > D-glucose
+		K21574	susB; glucan 1,4-alpha-glucosidase
+	starch > cyclodextrin
+		K00701	cgt; cyclomaltodextrin glucanotransferase
+	starch > maltodextrin
+		K01214	treX; isoamylase
+	starch > dextrin
+		K01176	amyA; alpha-amylase OR K07405 alpha-amylase OR K05343 treS; maltose alpha-D-glucosyltransferase / alpha-amylase
+		K01177	beta-amylase
+		K05992	amyM; maltogenic alpha-amylase OR K01208 nplT; cyclomaltodextrinase / maltogenic alpha-amylase / neopullulanase
+	POLYPHOSPHATE bidirectional
+	K00937	ppk; polyphosphate kinase OR K22468 ppk2; polyphosphate kinase
+	K01507	ppa; inorganic pyrophosphatase OR K15986 ppaC; manganese-dependent inorganic pyrophosphatase OR K06019 ppaX; pyrophosphatase PpaX
+	PHA/PHB synthesis/degradation
+	K00023	phbB; acetoacetyl-CoA reductase
+	K00626	phaA; acetyl-CoA C-acetyltransferase AND K03821 phaC; polyhydroxyalkanoate synthase subunit PhaC AND K22881 phaE; polyhydroxyalkanoate synthase subunit PhaE
+
 

KEGGDecoder/README.md

@@ -123,6 +123,15 @@ python Decode_and_Expand.py <FUNCTION_OUT.list> <HMM_OUT.list>
 
 Change Log
 ================================================================
+## V1.2
+Added several new pathways including:
+
+* PET degradation
+* carbon storage, related to starch/gylcogen & polyhydroxybutyrate
+* posphate storage, related to the reversible polyphosphate reaction. 
+
+Part of summer research with Sheyla Aviles.
+
 ## V1.1
 Correcting typos identified by Chris Neely. Adding more complete
 pathways components for amino acid biosynthesis identified by
@@ -131,7 +140,7 @@ Dr. Eric Webb
 * phenylalanine added K01713 pheC; cyclohexadienyl dehydratase OR K05359 ADT; arogenate/prephenate dehydratase OR K04518 pheA2; prephenate dehydratase
 * tyrosine added K00220 tyrC; cyclohexadieny/prephenate dehydrogenase OR K24018; cyclohexadieny/prephenate dehydrogenase OR K15226 tyrAa; arogenate dehydrogenase
 
-## V1.0.10##
+## V1.0.10 ##
 Added the 20 amino acids. In most instances, only the last step in converting precusor to amino acid is assessed (except for valine, isoleucine, leucine, and tryptophan). The following amino acids share detection pathways:
 
 * serine & glycine

KEGGDecoder/__init__.py

@@ -4,5 +4,5 @@
 """
 
 
-__version__ = "1.1"
+__version__ = "1.2"