Mercurial > repos > chmaramis > testirprofiler

changeset 10:5339fb9d8aee draft

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Deleted selected files
author chmaramis
date Sun, 18 Mar 2018 07:07:34 -0400
parents f4edb9437b95
children 14896ea6e180
files cmpb2016/pub_clono_JCDR3.py cmpb2016/pub_clono_JCDR3.xml cmpb2016/pub_clono_VCDR3.py cmpb2016/pub_clono_VCDR3.xml
diffstat 4 files changed, 0 insertions(+), 230 deletions(-) [+]
line wrap: on
line diff
--- a/cmpb2016/pub_clono_JCDR3.py	Sun Mar 18 07:06:56 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Feb 26 19:08:28 2016
-
-@author: chmaramis
-"""
-
-from __future__ import division
-import numpy as np
-from pandas import *
-from numpy import nan as NA
-import sys
-import time
-
-
-
-def publicJGeneClonoFunc(inputs,thres):
-    
-    clono=DataFrame()
-
-    for x in range(0,len(inputs),2):
-            cl = DataFrame()
-            cl = read_csv(inputs[x] , sep = '\t' , index_col = 0)
-            #tp = read_csv(inp_name, iterator=True, chunksize=5000,sep='\t', index_col=0 )
-            #cl = concat([chunk for chunk in tp]) 
-            
-            if (thres != 'null'):
-                cl = cl[cl['Reads'] > int(thres)]
-            
-            x1 = inputs[x+1].split('_')
-            
-            del cl['Reads']
-            cl.columns = [cl.columns[0], cl.columns[1], x1[0]+' '+cl.columns[2], x1[0]+' Relative '+cl.columns[3]]
-            
-            if clono.empty:
-                clono = cl
-            else:
-                clono = clono.merge(cl, how='outer', on=['J-GENE','AA JUNCTION'])
-    
-    
-    col = clono.columns
-    freqs = col.map(lambda x: 'Frequency' in x)
-    reads = col.map(lambda x: 'Reads/Total' in x)
-    
-    clono[col[freqs]] = clono[col[freqs]].fillna(0)
-    clono[col[reads]] = clono[col[reads]].fillna('0/*')
-    
-    clono['Num of Patients']= clono[col[freqs]].apply(lambda x: np.sum(x != 0), axis=1)
-
-    clono = clono[clono['Num of Patients'] > 1]
-
-    clono.index = range(1,len(clono)+1)
-    
-    return clono    
-
-
-if __name__ == '__main__':   
-
-    start=time.time()
-
-    # Parse input arguments    
-    arg = sys.argv[3:]
-    output = sys.argv[1]
-    thres = sys.argv[2]
-    
-    
-    # Execute basic function
-    mer = publicJGeneClonoFunc(arg,thres)
-    
-    # Save output to CSV files
-    if not mer.empty: 
-        mer.to_csv(output , sep = '\t') 
-        
-    # Print execution time
-    stop=time.time()
-    print('Runtime:' + str(stop-start))
--- a/cmpb2016/pub_clono_JCDR3.xml	Sun Mar 18 07:06:56 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<tool id="pubClonoJCDR3" name="Public J+CDR3 Clonotypes Computation" version="0.9">
-<description>Compute Public J+CDR3 Clonotypes</description>
-<command interpreter="python">
-pub_clono_JCDR3.py "$output1" "$Th.thres"
-#for x in $clono_files
-  "$x.clfile"
-  "$x.clfile.name"
-#end for
-</command>
-<inputs>
-	<conditional name="Th">
-	
-		<param name="thres_select" type="select" label="Remove Clonotypes With Reads Fewer Than Threshold?">
-			<option value="y">Yes</option>
-			<option value="n" selected="true">No</option>
-		</param>
-	
-		<when value="y">
-			<param name="thres" type="integer" size="4" value="1" min="1"  label="Keep Clonotypes with Number of Reads more than"/>
-		</when>
-	
-		<when value="n">
-			<param name="thres" type="hidden" value="null" />
-		</when>
-
-	</conditional>
-	<repeat name="clono_files" title="Files to be append" min="2">
-		<param name="clfile" type="data" label="Clonotype_File" format="tabular"/>
-	</repeat>
-
-</inputs>
-
-<outputs>
-	<data format="tabular" name="output1" label="Public_Clonotype"/>
-</outputs>
-<help>
-	This tool computes the public (J-gene, CDR3) Clonotypes among a number of patients along with their frequencies for each patient.
-</help>
-</tool>
--- a/cmpb2016/pub_clono_VCDR3.py	Sun Mar 18 07:06:56 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Feb 26 18:49:15 2016
-
-@author: chmaramis
-"""
-
-from __future__ import division
-import numpy as np
-from pandas import *
-from numpy import nan as NA
-import sys
-import time
-
-
-
-def publicVGeneClonoFunc(inputs,thres):
-    
-    clono=DataFrame()
-
-    for x in range(0,len(inputs),2):
-            cl = DataFrame()
-            cl = read_csv(inputs[x] , sep = '\t' , index_col = 0)
-            #tp = read_csv(inp_name, iterator=True, chunksize=5000,sep='\t', index_col=0 )
-            #cl = concat([chunk for chunk in tp]) 
-            
-            if (thres != 'null'):
-                cl = cl[cl['Reads'] > int(thres)]
-            
-            x1 = inputs[x+1].split('_')
-            
-            del cl['Reads']
-            cl.columns = [cl.columns[0], cl.columns[1], x1[0]+' '+cl.columns[2], x1[0]+' Relative '+cl.columns[3]]
-            
-            if clono.empty:
-                clono = cl
-            else:
-                clono = clono.merge(cl, how='outer', on=['V-GENE','AA JUNCTION'])
-    
-    
-    col = clono.columns
-    freqs = col.map(lambda x: 'Frequency' in x)
-    reads = col.map(lambda x: 'Reads/Total' in x)
-    
-    clono[col[freqs]] = clono[col[freqs]].fillna(0)
-    clono[col[reads]] = clono[col[reads]].fillna('0/*')
-    
-    clono['Num of Patients']= clono[col[freqs]].apply(lambda x: np.sum(x != 0), axis=1)
-
-    clono = clono[clono['Num of Patients'] > 1]
-
-    clono.index = range(1,len(clono)+1)
-    
-    return clono    
-
-
-if __name__ == '__main__':   
-
-    start=time.time()
-
-    # Parse input arguments    
-    arg = sys.argv[3:]
-    output = sys.argv[1]
-    thres = sys.argv[2]
-    
-    
-    # Execute basic function
-    mer = publicVGeneClonoFunc(arg,thres)
-    
-    # Save output to CSV files
-    if not mer.empty: 
-        mer.to_csv(output , sep = '\t') 
-        
-    # Print execution time
-    stop=time.time()
-    print('Runtime:' + str(stop-start))
--- a/cmpb2016/pub_clono_VCDR3.xml	Sun Mar 18 07:06:56 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<tool id="pubClonoVCDR3" name="Public V+CDR3 Clonotypes Computation" version="0.9">
-<description>Compute Public V+CDR3 Clonotypes</description>
-<command interpreter="python">
-pub_clono_VCDR3.py "$output1" "$Th.thres"
-#for x in $clono_files
-  "$x.clfile"
-  "$x.clfile.name"
-#end for
-</command>
-<inputs>
-	<conditional name="Th">
-	
-		<param name="thres_select" type="select" label="Remove Clonotypes With Reads Fewer Than Threshold?">
-			<option value="y">Yes</option>
-			<option value="n" selected="true">No</option>
-		</param>
-	
-		<when value="y">
-			<param name="thres" type="integer" size="4" value="1" min="1"  label="Keep Clonotypes with Number of Reads more than"/>
-		</when>
-	
-		<when value="n">
-			<param name="thres" type="hidden" value="null" />
-		</when>
-
-	</conditional>
-	<repeat name="clono_files" title="Files to be append" min="2">
-		<param name="clfile" type="data" label="Clonotype_File" format="tabular"/>
-	</repeat>
-
-</inputs>
-
-<outputs>
-	<data format="tabular" name="output1" label="Public_Clonotype"/>
-</outputs>
-<help>
-	This tool computes the public (V-gene, CDR3) Clonotypes among a number of patients along with their frequencies for each patient.
-</help>
-</tool>