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Pattern matching using awk from a file


 
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# 1  
Pattern matching using awk from a file

Hello, I have a very large file (DB_file.txt) with coordinate positions, example:


example for the DB_file.txt
Code:
chr1    1000    2000    chr1    10000    11000    3    281    0    0.459585414218248    0    0    0    1218    1    1.88650643678468    0    0    0    0.000000425582664277006    3.87833663319237    0.000000425597761316606    0.201115300038799    0.743522481235195    0.822936566866982
chr1    1000    2000    chr1    11000    12000    4    281    0    0.459585414218248    0    0    0    459    1    0.710924839477969    0    0    0    0.000000355375953311341    1.75327208538672    0.000000192399150742434    0.068194541602096    0.101318817290739    0.81707019750747
chr1    1000    2000    chr1    12000    13000    5    281    0    0.459585414218248    0    0    0    1415    1    2.19163104109222    0    0    0    0.000000310867653966458    3.44281554060217    0.000000377804900731428    0.128881860609444    0.263803805858084    0.81707019750747
chr1    1000    2000    chr1    13000    14000    1    281    0    0.459585414218248    0    0    0    437    1    0.676850010570529    0    0    0    0.000000285200375223444    1.49690344452761    0.000000164265976667856    0.335040184988013    0.776177861586765    0.837324774202159
chr1    1000    2000    chr1    14000    15000    1    281    0    0.459585414218248    0    0    0    530    1    0.820893605497437    0    0    0    0.000000271516726063383    1.60662404023105    0.000000176306406449545    0.322230259464951    0.799436461434159    0.850447555722604
chr1    1000    2000    chr1    16000    17000    1    281    0    0.459585414218248    0    0    0    490    1    0.758939371120272    0    0    0    0.000000253854147173018    1.41695624386548    0.000000155492795574155    0.343542270137564    0.75754917047966    0.828368055880824
 chr1    1000    2000   chr1    18000    19000    2    281    0    0.459585414218248    0    0    0    130    1    0.201351261725787    0    0    0    0.000000231422263301451    0.691389012939271    0.0000000758710869983566    0.119714987783608    0.152817308925748    0.81707019750747

I have a pattern file with the following:


Code:
chr1    1000    2000    chr1    10000    11000
chr1    1000    2000    chr1    11000    12000
chr1    1000    2000    chr1    12000    13000

For a single query, I am using the command:
Code:
awk '{if ($1 == "chr1" && $2 == "1000" && $3 == "2000" && $4 == "chr1" && $5 == "38000" && $6 == "39000") print $0}'  DB_file.txt

How can I do for all the patterns in a file ?
# 2  
Hi
try this
Code:
awk '
NR == FNR    {A[$1$2$3$4$5$6]; next}
$1$2$3$4$5$6 in A
' pattern.txt DB_file.txt

--- Post updated at 12:41 ---

in the same format pattern and db
Code:
awk '
NR == FNR    {A[$0]; len=length; next}
substr($0, 1, len) in A
' pattern.txt DB_file.txt

# 3  
Hello, Thanks for the reply. With the above code, only the last line of the pattern file got printed. Can you kindly check?



Code:

chr1    1000    2000    chr1    12000    13000    5    281    0    0.459585414218248    0    0    0    1415    1    2.19163104109222    0    0    0 0.000000310867653966458    3.44281554060217    0.000000377804900731428    0.128881860609444    0.263803805858084    0.81707019750747

# 4  
cat pattern.txt
Code:
chr1    1000    2000    chr1    10000    11000
chr1    1000    2000    chr1    11000    12000
chr1    1000    2000    chr1    12000    13000

cat DB_file.txt
Code:
chr1    1000    2000    chr1    10000    11000    3    281    0    0.459585414218248    0    0    0    1218    1    1.88650643678468    0    0    0    0.000000425582664277006    3.87833663319237    0.000000425597761316606    0.201115300038799    0.743522481235195    0.822936566866982
chr1    1000    2000    chr1    11000    12000    4    281    0    0.459585414218248    0    0    0    459    1    0.710924839477969    0    0    0    0.000000355375953311341    1.75327208538672    0.000000192399150742434    0.068194541602096    0.101318817290739    0.81707019750747
chr1    1000    2000    chr1    12000    13000    5    281    0    0.459585414218248    0    0    0    1415    1    2.19163104109222    0    0    0    0.000000310867653966458    3.44281554060217    0.000000377804900731428    0.128881860609444    0.263803805858084    0.81707019750747
chr1    1000    2000    chr1    13000    14000    1    281    0    0.459585414218248    0    0    0    437    1    0.676850010570529    0    0    0    0.000000285200375223444    1.49690344452761    0.000000164265976667856    0.335040184988013    0.776177861586765    0.837324774202159
chr1    1000    2000    chr1    14000    15000    1    281    0    0.459585414218248    0    0    0    530    1    0.820893605497437    0    0    0    0.000000271516726063383    1.60662404023105    0.000000176306406449545    0.322230259464951    0.799436461434159    0.850447555722604
chr1    1000    2000    chr1    16000    17000    1    281    0    0.459585414218248    0    0    0    490    1    0.758939371120272    0    0    0    0.000000253854147173018    1.41695624386548    0.000000155492795574155    0.343542270137564    0.75754917047966    0.828368055880824
 chr1    1000    2000   chr1    18000    19000    2    281    0    0.459585414218248    0    0    0    130    1    0.201351261725787    0    0    0    0.000000231422263301451    0.691389012939271    0.0000000758710869983566    0.119714987783608    0.152817308925748    0.81707019750747

cat test1.sh
Code:
#!/bin/bash
awk '
NR == FNR    {A[$1$2$3$4$5$6];next}
$1$2$3$4$5$6 in A
' pattern.txt DB_file.txt

Code:
./test1.sh
chr1    1000    2000    chr1    10000    11000    3    281    0    0.459585414218248    0    0    0    1218    1    1.88650643678468    0    0    0    0.000000425582664277006    3.87833663319237    0.000000425597761316606    0.201115300038799    0.743522481235195    0.822936566866982
chr1    1000    2000    chr1    11000    12000    4    281    0    0.459585414218248    0    0    0    459    1    0.710924839477969    0    0    0    0.000000355375953311341    1.75327208538672    0.000000192399150742434    0.068194541602096    0.101318817290739    0.81707019750747
chr1    1000    2000    chr1    12000    13000    5    281    0    0.459585414218248    0    0    0    1415    1    2.19163104109222    0    0    0    0.000000310867653966458    3.44281554060217    0.000000377804900731428    0.128881860609444    0.263803805858084    0.81707019750747

cat test2.sh
Code:
#!/bin/bash
awk '
NR == FNR    {A[$0]; len=length; next}
substr($0, 1, len) in A
' pattern.txt DB_file.txt

Code:
./test2.sh
chr1    1000    2000    chr1    10000    11000    3    281    0    0.459585414218248    0    0    0    1218    1    1.88650643678468    0    0    0    0.000000425582664277006    3.87833663319237    0.000000425597761316606    0.201115300038799    0.743522481235195    0.822936566866982
chr1    1000    2000    chr1    11000    12000    4    281    0    0.459585414218248    0    0    0    459    1    0.710924839477969    0    0    0    0.000000355375953311341    1.75327208538672    0.000000192399150742434    0.068194541602096    0.101318817290739    0.81707019750747
chr1    1000    2000    chr1    12000    13000    5    281    0    0.459585414218248    0    0    0    1415    1    2.19163104109222    0    0    0    0.000000310867653966458    3.44281554060217    0.000000377804900731428    0.128881860609444    0.263803805858084    0.81707019750747

This User Gave Thanks to nezabudka For This Post:

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