comparison vcf_snp.py @ 2:ea2f686dfd4a draft

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1:032d2c8cf8ae

#!/usr/bin/env python

#########################################################################################
#											#
# Name	      :	vcf_snp.py								#
# Version     : 0.1									#
# Project     : extract snp from vcf						#
# Description : Script to exctract snps		#
# Author      : Brigida Rusconi								#
# Date        : October 30 2015							#
#											#
#########################################################################################
#for replacement of a given value with NaN
#http://stackoverflow.com/questions/18172851/deleting-dataframe-row-in-pandas-based-on-column-value

# to remove any symbol and replace it with nan
#http://stackoverflow.com/questions/875968/how-to-remove-symbols-from-a-string-with-python

# for isin information
#http://pandas.pydata.org/pandas-docs/stable/indexing.html

# for selecting rows that have an indel:
#http://stackoverflow.com/questions/14247586/python-pandas-how-to-select-rows-with-one-or-more-nulls-from-a-dataframe-without



#------------------------------------------------------------------------------------------

#------------------------------------------------------------------------------------------


#read in file as dataframe
df =read_csv(input_file,sep='\t', dtype=object)
df=df.set_index(['#CHROM','POS'])

#need to fill na otherwise it cannot do boolean operations
df=df.fillna('--')
print "vcf " + str(df.index.size)
#------------------------------------------------------------------------------------------

# only columns with qbase and refbase in table
count_qbase=list(df.columns.values)
qindexes=[]
for i, v in enumerate(count_qbase):
    if 'ALT' in v:
        qindexes.append(i)
df2=df.iloc[:,qindexes]

#------------------------------------------------------------------------------------------
#pdb.set_trace()

#------------------------------------------------------------------------------------------

#save file with output name for fasta -o option and removes header and index
with open(output_file,'w') as output:
    df2.T.to_csv(output, sep='\t',header=False)
#------------------------------------------------------------------------------------------

2:ea2f686dfd4a

#!/usr/bin/env python

#########################################################################################
#											#
# Name	      :	vcf_snp.py								#
# Version     : 0.2									#
# Project     : extract snp from vcf						#
# Description : Script to exctract snps		#
# Author      : Brigida Rusconi								#
# Date        : November 02 2015							#
#											#
#########################################################################################

# If the position is identical to the reference it does not print the nucleotide. I have to retrieve it from the ref column.


#------------------------------------------------------------------------------------------

#------------------------------------------------------------------------------------------


#read in file as dataframe
df =read_csv(input_file,sep='\t', dtype=object)

#------------------------------------------------------------------------------------------

# only columns with qbase and refbase in table
#count_qbase=list(df.columns.values)
#qindexes=[]
#for i, v in enumerate(count_qbase):
#    if 'ALT' in v:
#        qindexes.append(i)
df2=df.iloc[:,3:5]
#pdb.set_trace()

#------------------------------------------------------------------------------------------
ref_list=[]
for i in range(0,df2.index.size):
    if df2.iloc[i,1]==".":
        ref_list.append(df2.iloc[i,0][0])
    else:
        ref_list.append(df2.iloc[i,1][0])
#pdb.set_trace()
#
##------------------------------------------------------------------------------------------
#
#save file with output name for fasta -o option and removes header and index
with open(output_file,'w') as output:
    output.write(df.columns.values[4] + '\t' + ''.join([str(i) for v,i in enumerate(ref_list)]))
##------------------------------------------------------------------------------------------