Revisions to Comparing two files using Unix and Awk

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occurred Jul 29, 2013 at 9:12

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edited Jul 28, 2013 at 23:52

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I need to compare two files, File1 and File2 (Separated by space) using 4 fields (Field 1, 2, 4 and 5 of File 1 with field1, 2, 4 and 5 of File2). Logic:

Logic:
If column 1, 2 and 4 of File 1 matches with column 1, 2 and 4 of File 2 and there is a mismatch at column 5 then both the lines from File 1 and File 2 are concatenated redirected as output. Therefore, the output file only contains those lines where Column 1, 2 and 4 of File1 and File2 matches and Column 5 does not match.

File1:

sc2/80 20 . A T 86 Pass N=2 F=5;U=4

sc2/60 55 . G T 76 Pass N=2 F=5;U=4

sc2/68 20 . T C 71 Pass N=2 F=5;U=4

sc2/24 24 . T G 31 Pass N=2 F=5;U=4

File2:

sc2/80 20 . A C 80 Pass N=2 F=5;U=4

sc2/60 55 . G C 72 Pass N=2 F=5;U=4

sc2/68 20 . T C 71 Pass N=2 F=5;U=4

sc2/10 24 . T G 31 Pass N=2 F=5;U=4File1:

sc2/40 59 . T G 31 Pass N=2 F=5;U=4

sc2/80         20      .        A       T         86       PASS     N=2     F=5;U=4
sc2/60         55      .        G       T         76       PASS     N=2     F=5;U=4 
sc2/68         20      .        T       C         71       PASS     N=2     F=5;U=4
sc2/24         24      .        T       G         31       PASS     N=2     F=5;U=4

sc2/24 24 . A G 38 Pass N=2 F=5;U=4File2:

OUTPUT:

sc2/80         20      .        A        C        80      PASS    N=2       F=5;U=4
sc2/60         55      .        G        C        72      PASS    N=2       F=5;U=4 
sc2/68         20      .        T        C        71      PASS    N=2       F=5;U=4 
sc2/10         24      .        T        G        31      PASS    N=2       F=5;U=4
sc2/40         59      .        T        G        31      PASS    N=2       F=5;U=4
sc2/24         24      .        A        G        38      PASS    N=2       F=5;U=4

sc2/80 20 . A T 86 Pass N=2 F=5;U=4 sc2/80 20 . A C 80 Pass N=2 F=5;U=4Output:

sc2/60 55 . G T 76 Pass N=2 F=5;U=4 sc2/60 55 . G C 72 Pass N=2 F=5;U=4

sc2/80         20      .        A       T        86      PASS     N=2      F=5;U=4
sc2/80         20      .        A       C        80      PASS     N=2      F=5;U=4

sc2/60         55      .        G       T        76      PASS     N=2      F=5;U=4 
sc2/60         55      .        G       C        72      PASS     N=2      F=5;U=4

I need to compare two files, File1 and File2 (Separated by space) using 4 fields (Field 1, 2, 4 and 5 of File 1 with field1, 2, 4 and 5 of File2). Logic: If column 1, 2 and 4 of File 1 matches with column 1, 2 and 4 of File 2 and there is a mismatch at column 5 then both the lines from File 1 and File 2 are concatenated redirected as output. Therefore, the output file only contains those lines where Column 1, 2 and 4 of File1 and File2 matches and Column 5 does not match.

File1:

sc2/80 20 . A T 86 Pass N=2 F=5;U=4

sc2/60 55 . G T 76 Pass N=2 F=5;U=4

sc2/68 20 . T C 71 Pass N=2 F=5;U=4

sc2/24 24 . T G 31 Pass N=2 F=5;U=4

File2:

sc2/80 20 . A C 80 Pass N=2 F=5;U=4

sc2/60 55 . G C 72 Pass N=2 F=5;U=4

sc2/68 20 . T C 71 Pass N=2 F=5;U=4

sc2/10 24 . T G 31 Pass N=2 F=5;U=4

sc2/40 59 . T G 31 Pass N=2 F=5;U=4

sc2/24 24 . A G 38 Pass N=2 F=5;U=4

OUTPUT:

sc2/80 20 . A T 86 Pass N=2 F=5;U=4 sc2/80 20 . A C 80 Pass N=2 F=5;U=4

sc2/60 55 . G T 76 Pass N=2 F=5;U=4 sc2/60 55 . G C 72 Pass N=2 F=5;U=4

I need to compare two files, File1 and File2 (Separated by space) using 4 fields (Field 1, 2, 4 and 5 of File 1 with field1, 2, 4 and 5 of File2).

Logic:
If column 1, 2 and 4 of File 1 matches with column 1, 2 and 4 of File 2 and there is a mismatch at column 5 then both the lines from File 1 and File 2 are concatenated redirected as output. Therefore, the output file only contains those lines where Column 1, 2 and 4 of File1 and File2 matches and Column 5 does not match.

File1:

sc2/80         20      .        A       T         86       PASS     N=2     F=5;U=4
sc2/60         55      .        G       T         76       PASS     N=2     F=5;U=4 
sc2/68         20      .        T       C         71       PASS     N=2     F=5;U=4
sc2/24         24      .        T       G         31       PASS     N=2     F=5;U=4

File2:

sc2/80         20      .        A        C        80      PASS    N=2       F=5;U=4
sc2/60         55      .        G        C        72      PASS    N=2       F=5;U=4 
sc2/68         20      .        T        C        71      PASS    N=2       F=5;U=4 
sc2/10         24      .        T        G        31      PASS    N=2       F=5;U=4
sc2/40         59      .        T        G        31      PASS    N=2       F=5;U=4
sc2/24         24      .        A        G        38      PASS    N=2       F=5;U=4

Output:

sc2/80         20      .        A       T        86      PASS     N=2      F=5;U=4
sc2/80         20      .        A       C        80      PASS     N=2      F=5;U=4

sc2/60         55      .        G       T        76      PASS     N=2      F=5;U=4 
sc2/60         55      .        G       C        72      PASS     N=2      F=5;U=4

deleted 26 characters in body

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edited Jul 28, 2013 at 23:51

Namrata

519
1
7
15

I need to compare two files, File1 and File2 (Separated by space) using 4 fields (Field 1, 2, 4 and 5 of File 1 with field1, 2, 4 and 5 of File2).

Logic:
Logic: If column 1, 2 and 4 of File 1 matches with column 1, 2 and 4 of File 2 and there is a mismatch at column 5 then both the lines from File 1 and File 2 are concatenated redirected as output. Therefore, the output file only contains those lines where Column 1, 2 and 4 of File1 and File2 matches and Column 5 does not match.

File1: File1:

sc2/80         20      .        A       T         86       PASS     N=2     F=5;U=4
sc2/60         55      .        G       T         76       PASS     N=2     F=5;U=4 
sc2/68         20      .        T       C         71       PASS     N=2     F=5;U=4
sc2/24         24      .        T       G         31       PASS     N=2     F=5;U=4

sc2/80 20 . A T 86 Pass N=2 F=5;U=4

File2: sc2/60 55 . G T 76 Pass N=2 F=5;U=4

sc2/80         20      .        A        C        80      PASS    N=2       F=5;U=4
sc2/60         55      .        G        C        72      PASS    N=2       F=5;U=4 
sc2/68         20      .        T        C        71      PASS    N=2       F=5;U=4 
sc2/10         24      .        T        G        31      PASS    N=2       F=5;U=4
sc2/40         59      .        T        G        31      PASS    N=2       F=5;U=4
sc2/24         24      .        A        G        38      PASS    N=2       F=5;U=4

sc2/68 20 . T C 71 Pass N=2 F=5;U=4

Output: sc2/24 24 . T G 31 Pass N=2 F=5;U=4

sc2/80         20      .        A       T        86      PASS     N=2      F=5;U=4
sc2/80         20      .        A       C        80      PASS     N=2      F=5;U=4

sc2/60         55      .        G       T        76      PASS     N=2      F=5;U=4 
sc2/60         55      .        G       C        72      PASS     N=2      F=5;U=4

File2:

sc2/80 20 . A C 80 Pass N=2 F=5;U=4

sc2/60 55 . G C 72 Pass N=2 F=5;U=4

sc2/68 20 . T C 71 Pass N=2 F=5;U=4

sc2/10 24 . T G 31 Pass N=2 F=5;U=4

sc2/40 59 . T G 31 Pass N=2 F=5;U=4

sc2/24 24 . A G 38 Pass N=2 F=5;U=4

OUTPUT:

sc2/80 20 . A T 86 Pass N=2 F=5;U=4 sc2/80 20 . A C 80 Pass N=2 F=5;U=4

sc2/60 55 . G T 76 Pass N=2 F=5;U=4 sc2/60 55 . G C 72 Pass N=2 F=5;U=4

I need to compare two files, File1 and File2 (Separated by space) using 4 fields (Field 1, 2, 4 and 5 of File 1 with field1, 2, 4 and 5 of File2).

Logic:
If column 1, 2 and 4 of File 1 matches with column 1, 2 and 4 of File 2 and there is a mismatch at column 5 then both the lines from File 1 and File 2 are concatenated redirected as output. Therefore, the output file only contains those lines where Column 1, 2 and 4 of File1 and File2 matches and Column 5 does not match.

File1:

sc2/80         20      .        A       T         86       PASS     N=2     F=5;U=4
sc2/60         55      .        G       T         76       PASS     N=2     F=5;U=4 
sc2/68         20      .        T       C         71       PASS     N=2     F=5;U=4
sc2/24         24      .        T       G         31       PASS     N=2     F=5;U=4

File2:

sc2/80         20      .        A        C        80      PASS    N=2       F=5;U=4
sc2/60         55      .        G        C        72      PASS    N=2       F=5;U=4 
sc2/68         20      .        T        C        71      PASS    N=2       F=5;U=4 
sc2/10         24      .        T        G        31      PASS    N=2       F=5;U=4
sc2/40         59      .        T        G        31      PASS    N=2       F=5;U=4
sc2/24         24      .        A        G        38      PASS    N=2       F=5;U=4

Output:

sc2/80         20      .        A       T        86      PASS     N=2      F=5;U=4
sc2/80         20      .        A       C        80      PASS     N=2      F=5;U=4

sc2/60         55      .        G       T        76      PASS     N=2      F=5;U=4 
sc2/60         55      .        G       C        72      PASS     N=2      F=5;U=4

I need to compare two files, File1 and File2 (Separated by space) using 4 fields (Field 1, 2, 4 and 5 of File 1 with field1, 2, 4 and 5 of File2). Logic: If column 1, 2 and 4 of File 1 matches with column 1, 2 and 4 of File 2 and there is a mismatch at column 5 then both the lines from File 1 and File 2 are concatenated redirected as output. Therefore, the output file only contains those lines where Column 1, 2 and 4 of File1 and File2 matches and Column 5 does not match.

File1:

sc2/80 20 . A T 86 Pass N=2 F=5;U=4

sc2/60 55 . G T 76 Pass N=2 F=5;U=4

sc2/68 20 . T C 71 Pass N=2 F=5;U=4

sc2/24 24 . T G 31 Pass N=2 F=5;U=4

File2:

sc2/80 20 . A C 80 Pass N=2 F=5;U=4

sc2/60 55 . G C 72 Pass N=2 F=5;U=4

sc2/68 20 . T C 71 Pass N=2 F=5;U=4

sc2/10 24 . T G 31 Pass N=2 F=5;U=4

sc2/40 59 . T G 31 Pass N=2 F=5;U=4

sc2/24 24 . A G 38 Pass N=2 F=5;U=4

OUTPUT:

sc2/80 20 . A T 86 Pass N=2 F=5;U=4 sc2/80 20 . A C 80 Pass N=2 F=5;U=4

sc2/60 55 . G T 76 Pass N=2 F=5;U=4 sc2/60 55 . G C 72 Pass N=2 F=5;U=4

Fix formatting.

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edited Jul 28, 2013 at 23:50

user26112

I need to compare two files, File1 and File2 (Separated by space) using 4 fields (Field 1, 2, 4 and 5 of File 1 with field1, 2, 4 and 5 of File2). Logic:

Logic:
If column 1, 2 and 4 of File 1 matches with column 1, 2 and 4 of File 2 and there is a mismatch at column 5 then both the lines from File 1 and File 2 are concatenated redirected as output. Therefore, the output file only contains those lines where Column 1, 2 and 4 of File1 and File2 matches and Column 5 does not match.

File1:File1:

File2:File2:

OUTPUT:Output:

added 60 characters in body

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edited Jul 28, 2013 at 23:49

jordanm

43.6k
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asked Jul 28, 2013 at 23:45

Namrata

519
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15

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