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# 1  
Old 09-30-2016
awk to compare each file in two directores by storing in variable
In the below bash I am trying to read each file from a specific directory into a variable REF or VAL. Then use those variables in an awk to compare each matching file from REF and VAL. The filenames in the REF are different then in the VAL, but have a common id up until the _ I know the awk portion works as I can run files through them manually. However, I am not sure if I am doing the variable part correctly. Thank you Smilie.

The two variables are:

REF comes from /home/cmccabe/Desktop/comparison/reference/10bp and is 3 files:

Code:
 S1234_ref.txt
 A5678_ref.txt
 T1111_ref.txt

VAR comes from /home/cmccabe/Desktop/comparison/validation/files
 and is 3 files:

Code:
 S1234_panel.vcf
 A5678_panel.vcf
 T1111_panel.vcf

So, S1234_ref.txt would be REF and S1234_panel.vcf would be VAL, then those two files would be compared. I think I am close but not too sure about the variables.

Code:
 REF=/home/cmccabe/Desktop/comparison/reference/10bp
VAL=/home/cmccabe/Desktop/comparison/validation/files
awk -F'\t' -v OFS='\t' 'FNR==1 { next }
      FNR == NR { file1[$2,$4,$5] = $2 FS $4 FS $5 }
      FNR != NR { file2[$2,$4,$5] = $2 FS $4 FS $5 }
            END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
            print "Missing in Reference but found in IDP:"; for (k in file2) if (!(k in file1)) print file2[k]
            print "Missing in IDP but found in Reference:"; for (k in file1) if (!(k in file2)) print file1[k]
      }'$REF $VAL > /home/cmccabe/Desktop/comparison/ref_val/concordance.txt

Last edited by cmccabe; 09-30-2016 at 04:01 PM.. Reason: added details
# 2  
Old 09-30-2016
Hello cmccabe,

Could you please try to keep those both variables values into a single Input_file like as follows.
Code:
cat Input_file
S1234_ref.txt S1234_panel.vcf
A5678_ref.txt A5678_panel.vcf
T1111_ref.txt T1111_panel.vcf

Also to get the above Input_file you could use paste var_file ref_file > Input_file
Then you could try to read their values by a loop and try to put your awkinside it.
Code:
while read file1 file2
      awk '{your_logic}' $file1  $file2
done < "Input_file"

Could you please try it out and let us know how it goes then. If you have more requirements in here, kindly post with full details on same.

Thanks,
R. Singh
Last edited by RavinderSingh13; 09-30-2016 at 04:47 PM..
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
# 3  
Old 09-30-2016
Not sure if I follow completly, but here is what I did:

/home/cmccabe/Desktop/comparison/ref_val/out

out file used as input
Code:
F13_ref_FP_10bp.txt F13_epilepsy.vcf
M29_ref_FP_10bp.txt M29_epilepsy
H68_ref_FP_10bp.txt H68_marfan.vcf
T42_ref_FP_10bp.txt T42_epilepsy.vcf
H19_ref_FP_10bp.txt H19_marfan.vcf
T48_ref_FP_10bp.txt T48_marfan.vcf

Code:
while read file1 file2
         awk -F'\t' -v OFS='\t' 'FNR==1 { next }
         FNR == NR { file1[$2,$4,$5] = $2 FS $4 FS $5 }
         FNR != NR { file2[$2,$4,$5] = $2 FS $4 FS $5 }
              END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
              print "Missing in Reference but found in IDP:"; for (k in file2) if (!(k in file1)) print file2[k]
              print "Missing in IDP but found in Reference:"; for (k in file1) if (!(k in file2)) print file1[k]
}'/home/cmccabe/Desktop/comparison/reference/10bp/$file1 /home/cmccabe/Desktop/comparison/validation/files/$file2 > /home/cmccabe/Desktop/comparison/ref_val/concordance.txt
done < "/home/cmccabe/Desktop/comparison/ref_val/out"

Code:
I give the full path to each:
file1
file2
out

Thank you Smilie.
# 4  
Old 09-30-2016
Quote:
Originally Posted by cmccabe
Not sure if I follow completly, but here is what I did:

/home/cmccabe/Desktop/comparison/ref_val/out

out file used as input
Code:
F13_ref_FP_10bp.txt F13_epilepsy.vcf
M29_ref_FP_10bp.txt M29_epilepsy
H68_ref_FP_10bp.txt H68_marfan.vcf
T42_ref_FP_10bp.txt T42_epilepsy.vcf
H19_ref_FP_10bp.txt H19_marfan.vcf
T48_ref_FP_10bp.txt T48_marfan.vcf

Code:
while read file1 file2
         awk -F'\t' -v OFS='\t' 'FNR==1 { next }
         FNR == NR { file1[$2,$4,$5] = $2 FS $4 FS $5 }
         FNR != NR { file2[$2,$4,$5] = $2 FS $4 FS $5 }
              END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
              print "Missing in Reference but found in IDP:"; for (k in file2) if (!(k in file1)) print file2[k]
              print "Missing in IDP but found in Reference:"; for (k in file1) if (!(k in file2)) print file1[k]
}'/home/cmccabe/Desktop/comparison/reference/10bp/$file1 /home/cmccabe/Desktop/comparison/validation/files/$file2 > /home/cmccabe/Desktop/comparison/ref_val/concordance.txt
done < "/home/cmccabe/Desktop/comparison/ref_val/out"

Code:
I give the full path to each:
file1
file2
out

Thank you Smilie.
Hello cmccabe,

As we have requested mutiple times, kindly do mention complete details about what's happening and what's not. Though you have used code as I suggested in post#2 but you haven't mention either that approach worked or not. Because you haven't showed us what are there in those Input_files(how Input_file looks with sample data) it is difficult to tell that you command will work or not, please let us know the complete details about your requirements with sample Input_file and ecpected output of your requirements with error messages(if any) you code by running any suggestions or your own codes, I hope this helps.

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
# 5  
Old 09-30-2016
I am not sure what you mean by create an input file, I created the input as the filenames of REF in $1 of and the filenames of VAL in $2. I then gave the full path to the location of each filename in $1 and the full path to each filename in $2. After giving the full paths to file1 file2 and input, I used the awk, it ran but nothing happened and no output was produced. I was trying to use your code but just misunderstood it. I hope this helps and thank you Smilie.
# 6  
Old 10-01-2016
How about
Code:
for FN in $REF; do awk '...' $FN ${FN%%_*}*.vcf ; done

You may need to add the path to the .vcf files, though.

I have to second RavinderSingh13 in that all your specifications/requests need to be WAY clearer and more detailed/data driven!
This User Gave Thanks to RudiC For This Post:
cmccabe
# 7  
Old 10-01-2016
@RudiC and @RavinderSingh13, thank you both for all of your help.

it looks like the script reads all the vcf files from REF and puts them in a variable FN. How do the txt files from VAL get used by the awk. The awk looks at each REF file and compares it to each VAL file looking for what's common and what's different. If a difference is found it identifies which file the missing data came from. The awk portion works on individual files, but I have over 500to compare so a loop would help, however that is what I need help with Smilie.

REF there are 250 files all located at /home/cmccabe/Desktop/comparison/reference/10bp

Code:
F13_ref_FP_10bp.txt
H19_ref_FP_10bp.txt

Data structure in REF
Code:
Chr    Start    End    Ref    Alt    Func.refGene    Gene.refGene    Coverage    Score    A(#F,#R)    C(#F,#R)    G(#F,#R)    T(#F,#R)    Ins(#F,#R)    Del(#F,#R)    SNP    Mutation    Frequency    Sanger
12    52200340    52200340    A    C    exonic    SCN8A    4129    28.3    1560;1672    413;453    0;0    0;0    0;2    31;0        c.[5070A>C]+[=]    20.97    
2    51254914    51254914    C    T    exonic    NRXN1    1562    25.5    0;0    536;218    0;0    574;234    0;0    0;0        c.[498G>A]+[=]    51.73    
X    67433722    67433722    C    T    exonic    OPHN1    2747    25.6    0;0    46;37    0;0    1211;1443    1;8    5;5        c.[579G>A]+[579G>A]    96.61

VAL there are 250 files all located at /home/cmccabe/Desktop/comparison/validation/files

Code:
F13_epilepsy.vcf
H19_marfan.vcf

Data structure in VAL
Code:
Chr    Start    End    Ref    Alt    Func.refGene    Gene.refGene    GeneDetail.refGene    ExonicFunc.refGene    AAChange.refGene    avsnp147    PopFreqMax    1000G_ALL    1000G_AFR    1000G_AMR    1000G_EAS    1000G_EUR    1000G_SAS    ExAC_ALL    ExAC_AFR    ExAC_AMR    ExAC_EAS    ExAC_FIN    ExAC_NFE    ExAC_OTH    ExAC_SAS    ESP6500siv2_ALL    ESP6500siv2_AA    ESP6500siv2_EA    CG46    dpsi_max_tissue    dpsi_zscore    SIFT_score    SIFT_pred    Polyphen2_HDIV_score    Polyphen2_HDIV_pred    Polyphen2_HVAR_score    Polyphen2_HVAR_pred    LRT_score    LRT_pred    MutationTaster_score    MutationTaster_pred    MutationAssessor_score    MutationAssessor_pred    CLINSIG    CLNDBN    CLNACC    CLNDSDB    CLNDSDBID    Quality    Reads    Zygosity    Phred    Classification    HGMD    Sanger
chr1    43395635    43395635    C    T    exonic    SLC2A1    .    synonymous SNV    SLC2A1:NM_006516:exon5:c.588G>A:p.P196P    rs2229682    0.23    0.12    0.024    0.21    0.08    0.19    0.15    0.18    0.044    0.19    0.074    0.23    0.21    0.19    0.19    0.15    0.049    0.2    0.12    -0.1558    -0.594    .    .    .    .    .    .    .    .    .    .    .    .    Benign    not_specified    RCV000081436.5    MedGen    CN169374    GOOD    399    het    19
chr1    43396414    43396414    G    A    exonic    SLC2A1    .    synonymous SNV    SLC2A1:NM_006516:exon4:c.399C>T:p.C133C    rs11537641    0.24    0.14    0.08    0.21    0.1    0.19    0.16    0.19    0.094    0.2    0.098    0.24    0.21    0.2    0.2    0.16    0.096    0.2    0.14    -0.0227    -0.121    .    .    .    .    .    .    .    .    .    .    .    .    Benign    not_specified    RCV000081433.6    MedGen    CN169374    GOOD    400    het    21
chr1    172410967    172410967    G    A    exonic    PIGC    .    nonsynonymous SNV    PIGC:NM_002642:exon2:c.796C>T:p.P266S,PIGC:NM_153747:exon2:c.796C>T:p.P266S    rs1063412    0.66    0.45    0.06    0.54    0.66    0.6    0.57    0.55    0.14    0.64    0.64    0.59    0.58    0.57    0.57    0.42    0.15    0.56    0.41    .    .    0.13    T    1.0    D    1.0    D    0.000    D    0.000    P    1.515    L    .    .    .    .    .    GOOD    399    het    19

desired output (example not using these files that compares a REF file to a VAL file and finds what's in common, what's different, and where the difference comes from, it includes some additional data as well from another script)

Code:
Match:
Chr    Start    Ref    Alt    Func.refGene    Gene.refGene    Quality    Reads    Zygosity    Phred
chr15    68521889    C    T    exonic    CLN6    GOOD    50    het    4
chr7    147183143    A    G    intronic    CNTNAP2    GOOD    382    het    22
chr2    167099158    A    G    exonic    SCN9A    GOOD    210    hom    55
Missing in Reference but found in IDP:
Chr    Start    Ref    Alt    Func.refGene    Gene.refGene    Quality    Reads    Zygosity    Phred
chr2    51666313    T    C    intergenic    NRXN1,NONE    GOOD    108    het    7
chr2    166903445    T    C    exonic    SCN1A    GOOD    400    het    28
Missing in IDP but found in Reference:
Chr    Start    Ref    Alt    Func.refGene    Gene.refGene    Mutation Call    Coverage    Score    Mutant Allele Frequency    A(#F,#R)    C(#F,#R)    G(#F,#R)    T(#F,#R)    ins(#F,#R)    del(#F,#R)    SNP db_ref    Region    
2    166210776    C    T    exonic    SCN2A    c.[2994C>T]+[=]    3095    23.1    24.56    0:0    1158:1177    0;0    457;303    1;0    0;0        No low coverage
7    148106478    -    GT    intronic    CNTNAP2    c.3716-5_3716-4insGT    4168    28.6    51.01    0;0    0;1    0;0    2199;1967    1129;997    0;1    rs60451214    No low

I hope this helps and apologize for the long post but think these are all the details. Thank you Smilie.
Last edited by cmccabe; 10-01-2016 at 10:49 AM.. Reason: added details
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