Mercurial > repos > davidvanzessen > shm_csr

changeset 26:ce25fb581ca3 draft

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Uploaded
author davidvanzessen
date Mon, 05 Dec 2016 11:00:13 -0500
parents 8d1c4c75f81b
children 69baebd10e54
files gene_identification.py shm_csr.py wrapper.sh
diffstat 3 files changed, 12 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/gene_identification.py	Mon Dec 05 08:26:01 2016 -0500
+++ b/gene_identification.py	Mon Dec 05 11:00:13 2016 -0500
@@ -164,7 +164,8 @@
 varsInCM = 0
 varsInCE = 0
 
-
+def round_int(val):
+	return int(round(val))
 
 first = True
 seq_write_count=0
@@ -193,27 +194,27 @@
 				ca1hits = currentIDHits["ca1"]
 				ca2hits = currentIDHits["ca2"]
 				if ca1hits >= ca2hits:
-					o.write(ID + "\tIGA1\t" + str(int(ca1hits / varsInCA * 100)) + "\t" + str(int(cahits / possibleca * 100)) + "\t" + start_location[ID + "_ca"] + "\n")
+					o.write(ID + "\tIGA1\t" + str(round_int(ca1hits / varsInCA * 100)) + "\t" + str(round_int(cahits / possibleca * 100)) + "\t" + start_location[ID + "_ca"] + "\n")
 				else:
-					o.write(ID + "\tIGA2\t" + str(int(ca2hits / varsInCA * 100)) + "\t" + str(int(cahits / possibleca * 100)) + "\t" + start_location[ID + "_ca"] + "\n")
+					o.write(ID + "\tIGA2\t" + str(round_int(ca2hits / varsInCA * 100)) + "\t" + str(round_int(cahits / possibleca * 100)) + "\t" + start_location[ID + "_ca"] + "\n")
 			elif cghits >= cahits and cghits >= cmhits and cghits >= cehits: #its a cg gene
 				cg1hits = currentIDHits["cg1"]
 				cg2hits = currentIDHits["cg2"]
 				cg3hits = currentIDHits["cg3"]
 				cg4hits = currentIDHits["cg4"]
 				if cg1hits >= cg2hits and cg1hits >= cg3hits and cg1hits >= cg4hits: #cg1 gene
-					o.write(ID + "\tIGG1\t" + str(int(cg1hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+					o.write(ID + "\tIGG1\t" + str(round_int(cg1hits / varsInCG * 100)) + "\t" + str(round_int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 				elif cg2hits >= cg1hits and cg2hits >= cg3hits and cg2hits >= cg4hits: #cg2 gene
-					o.write(ID + "\tIGG2\t" + str(int(cg2hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+					o.write(ID + "\tIGG2\t" + str(round_int(cg2hits / varsInCG * 100)) + "\t" + str(round_int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 				elif cg3hits >= cg1hits and cg3hits >= cg2hits and cg3hits >= cg4hits: #cg3 gene
-					o.write(ID + "\tIGG3\t" + str(int(cg3hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+					o.write(ID + "\tIGG3\t" + str(round_int(cg3hits / varsInCG * 100)) + "\t" + str(round_int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 				else: #cg4 gene
-					o.write(ID + "\tIGG4\t" + str(int(cg4hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+					o.write(ID + "\tIGG4\t" + str(round_int(cg4hits / varsInCG * 100)) + "\t" + str(round_int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 			else: #its a cm or ce gene
 				if cmhits >= cehits:
-					o.write(ID + "\tIGM\t100\t" + str(int(cmhits / possiblecm * 100)) + "\t" + start_location[ID + "_cm"] + "\n")
+					o.write(ID + "\tIGM\t100\t" + str(round_int(cmhits / possiblecm * 100)) + "\t" + start_location[ID + "_cm"] + "\n")
 				else:
-					o.write(ID + "\tIGE\t100\t" + str(int(cehits / possiblece * 100)) + "\t" + start_location[ID + "_ce"] + "\n")
+					o.write(ID + "\tIGE\t100\t" + str(round_int(cehits / possiblece * 100)) + "\t" + start_location[ID + "_ce"] + "\n")
 			seq_write_count += 1
 
 print "Time: %i" % (int(time.time() * 1000) - starttime)
--- a/shm_csr.py	Mon Dec 05 08:26:01 2016 -0500
+++ b/shm_csr.py	Mon Dec 05 11:00:13 2016 -0500
@@ -85,7 +85,7 @@
 	AALength = 64
 
 AA_mutation = [0] * AALength
-AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]}
+AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "IGE": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]}
 AA_mutation_empty = AA_mutation[:]
 
 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
--- a/wrapper.sh	Mon Dec 05 08:26:01 2016 -0500
+++ b/wrapper.sh	Mon Dec 05 11:00:13 2016 -0500
@@ -578,7 +578,7 @@
 echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transitions_all_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output
-echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output
+echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transitions_IGG_sum.txt' download='transitions_IGG_sum.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transitions_IGG1_sum.txt' download='transitions_IGG1_sum.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transitions_IGG2_sum.txt' download='transitions_IGG2_sum.txt' >Download</a></td></tr>" >> $output