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I have very large sizes tab-delimited .vcf files and want to match these two / or 3 files based on their position and print to a new .csv file

File structures:

File_1: tab-delimited file (.vcf) and its as column names as follows (line number 3439) #CHROM POS ID REF ALT QUAL FILTER INFO

File 2: same as file_1 column names

(line number 3407) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE_1 SAMPLE_2 .....

In file_2, column 7 (INFO) contain many substrings like AC=46,2;AF=0.958,0.042;AN=48;DP=269;ExcessHet=3.0103;FS=0.000;InbreedingCoeff=0.5411;MLEAC=92,4;MLEAF=1.00,0.083;QD=25.36;SOR=2.488 from these strings , have to print only information of AC=, AF=, AN=, DP=

Desired output files to generate:

  1. position matched in two of files: common_position_matched.csv

if I have more than 3 files also, the output should be one file and important thing, if a position column (1-POS) only matched only in 2 files and 1st file line should be NA NA NA

file_1  CHROM  POS    REF  ALT     file_2 #CHROM  POS      REF  ALT  INFO

1       22    10511521  C     T         1    22  10511521   C    T   AC=46,2 AF=0.958,0.042 AN=48 DP=269  
2       22   10510544   G     A         2    22  10510544   G    A   AC=49,2 AF=0.958,0.042 AN=89 DP=536  
3       22   10515068  AGAT,T AGAT,AT   3    22  10515068   AAA  AAAGG,A,GAA AC=100  AF=0.958,0.042 AN=62 DP=123  
4       22   10515118  A G,   TAA       4    22  10515118   AG,  TAA AC=32   AF=0.958,0.042 AN=45 DP=500  
5       22   10515118  AAAG   A         5    22  10515118   AATG A   AC=50   AF=0.958,0.042 AN=49 DP=129

note: while doing matching, not removing the duplicates, because in the same position there may be an addition or sometimes it may be deletion.

  1. unique position of each file, in tab-delimited

output: File1_unique.csv and File2_unique.csv etc.

so far was able to read the file and match them according to position and print the output, but was not able to write efficient code

import pandas as pd
df1 = pd.read_csv("File1_3.vcf",sep='\t',usecols = ['POS']) ## Reading file1
df2 = pd.read_csv("file2_3.vcf", sep="\t", usecols = ['POS']) ## Reading file2
df3 = pd.concat([df1,df2], sort=True) ## Combining both the dataframes
df4 = df3.drop_duplicates(keep=False) ## Dropping the duplicates (intersect)
df4.to_csv("c3-UniquePosition_of_bothData.csv", sep="\t", index=False, header=True) ## Writing the unique to both
df1_Uni_file1_c3Posi = pd.merge(df4, df1, on='POS', how='inner') ## Identifying the unique position of File1 
df2_Uni_File2_c3Posi = pd.merge(df4, df2, on='POS', how='inner') ## Identifying the unique position of File2
df_File1_File2_common_c3Posi = pd.merge(df1, df2, on='POS', how='inner') # Identifying the common chr-position of File1 and File2```  

Program 2: (giving original file without editting)
import pandas as pd
df1= pd.read_csv("File1_22.vcf.gz", sep="\t", skiprows=3438, usecols = [0,1,2,3,4])
df2 = pd.read_csv("File2_22.vcf.gz", sep="\t", skiprows=3406, usecols = [0,1,3,4,7])
#writing the output files
#df1.to_csv("File1_c22.csv")
#df2.to_csv("File2_c22.csv")
#mergeing
df3 = pd.merge(df1, df2, on='POS', how='inner', sort=True)
df3.to_csv("common_position.csv", sep=",", index=False, header=True)
#df3 = pd.concat([df1,df2], axis=1).to_csv('check1.csv') # this command join multiple output to single output

Could any one give efficient python pandas script, to do this

Thanks All

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  • 2
    $\begingroup$ I suggest you reformat your post to make it clearer. Right now I feel reluctant to even read it as it is extensive and not well formatted. maybe this is just me, but probably not. $\endgroup$ – ATpoint Feb 12 at 14:08
  • $\begingroup$ Beyond reformatting, it would be great if you can clarify the question. What are the tab-delimited files? They appear to be lists of mutations, but can you confirm that? And what exactly do you mean by position matching? You provide many examples but it would be great if you can clarify in text exactly what those examples are meant to show. $\endgroup$ – alizabr Feb 12 at 18:03
  • $\begingroup$ @ATpo and alizbar, I had reformated the question as much I can, could you people give me some solution $\endgroup$ – Nitha Feb 14 at 5:57

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