changeset 11:14896ea6e180 draft

Deleted selected files

--- a/cmpb2016/top10_CDR3_exact_pairing.py	Sun Mar 18 07:07:34 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Mon Apr 18 09:48:00 2016
-
-@author: chmaramis
-"""
-
-import pandas as pd
-import numpy as np
-import sys
-
-
-if __name__ == "__main__":
-    
-    clonosFN = sys.argv[1]
-    outFN = sys.argv[2]
-    
-    Cl = pd.read_csv(clonosFN,sep='\t',index_col=0)
-    T10 = Cl[:10].copy()
-    
-    aa_junction = np.array(T10['AA JUNCTION'])
-    geneCol = [x for x in T10.columns if x.upper().endswith('GENE')][0]
-    
-    vG_unique = np.unique(Cl[geneCol])
-    noVG = len(vG_unique)
-    
-    F = np.zeros((noVG,20))
-    
-    for i in range(0,10):
-        taa = T10['AA JUNCTION'][i+1]
-        sameAA = np.where(Cl['AA JUNCTION'] == taa)[0]+1
-        if Cl[geneCol][sameAA[0]] != T10[geneCol][i+1]:
-            print('We have a problem here!')
-    
-        # Make original Gene -1    
-        #orGene = Cl['V-GENE'][sameAA[0]]
-        #orGeneUn = np.where(vG_unique == orGene)[0][0]
-        #F[orGeneUn,i] = -1
-        
-        # Other Genes
-        for j in range(0,len(sameAA)):
-            othGene = Cl[geneCol][sameAA[j]]
-            othRead = Cl['Reads'][sameAA[j]]
-            othFreq = Cl['Frequency %'][sameAA[j]]
-            orGeneUn = np.where(vG_unique == othGene)[0][0]
-            F[orGeneUn,2*i] += othRead
-            F[orGeneUn,2*i+1] += othFreq
-         
-         
-    K = list(aa_junction+' Reads') 
-    L = list(aa_junction+' Freq. %')
-    columns = [val for pair in zip(K,L) for val in pair]
-    
-    D = pd.DataFrame(F,columns=columns,index=vG_unique)
-    D.to_csv(outFN,sep='\t')
-    

--- a/cmpb2016/top10_CDR3_exact_pairing.xml	Sun Mar 18 07:07:34 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-<tool id="top10CDR3exPair" name="Top10 CDR3 Exact Pairing" version="0.9">
-<description>Pair CDR3 of top10 clonotypes with combined genes</description>
-<command interpreter="python">
-top10_CDR3_exact_pairing.py "$clonos" "$out"
-</command>
-<inputs>
-<param format="txt" name="clonos" type="data" label="Full List of Clonotypes"/>
-</inputs>
-
-<outputs>
-<data format="tabular" name="out" label="${clonos.name}_top10CDR3_exactPairing"/>
-</outputs>
-<help>
-Lists the genes with which the AA Junctions (CDR3) of the Top-10 clonotypes are combined. Works for both V-Gene and J-Gene clonotypes. 
-</help>
-</tool>
-