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How to join one file with multiple files in a directory in UNIX?

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Top Forums Shell Programming and Scripting How to join one file with multiple files in a directory in UNIX?
# 8  
Old 04-23-2015
Quote:
Originally Posted by sajmar
As I mentioned, I have 300 files in the folders which are like file2 and they all have the same ending file name which is *.geno . now each of these file have different rows. I want to know how many of the id fields like (gi|358484521|ref|NW_003764373.1|) are present in each of these 300 files.
Your requirement is unclear to me. In the example you gave there is no relation between column 2 and 3 in the output file..

---
*EDIT*
OK I see you have just edited your post #1 and now the requirements are different. Please do not do that, it makes the thread hard to follow. And please try to get your specification right from the start.

So you mean something like this then?
Code:
awk 'NR==FNR{A[$2]=$0; next} $1 in A{print A[$1], $0}' file1 *.geno

or try an xargs approach...
Last edited by Scrutinizer; 04-23-2015 at 03:09 PM..
This User Gave Thanks to Scrutinizer For This Post:
sajmar
# 9  
Old 04-23-2015
Sorry Scrutinize, if I put you in the wrong way. this time the command works well. But If I need to put it inside loop, this code did not work
Code:
ls *.geno | while read FN;  awk 'NR==FNR{A[$2]=$0; next} $1 in A{print A[$1], $0}' unlocol_accessions $FN > ${FN/geno/geno2}; done

do you have any suggestion for putting your command in loop?
# 10  
Old 04-23-2015
Quote:
Originally Posted by sajmar
Sorry Scrutinize, if I put you in the wrong way. this time the command works well. But If I need to put it inside loop, this code did not work
Code:
ls *.geno | while read FN;  awk 'NR==FNR{A[$2]=$0; next} $1 in A{print A[$1], $0}' unlocol_accessions $FN > ${FN/geno/geno2}; done

do you have any suggestion for putting your command in loop?
Instead of saying "code did not work" it would help everyone reading your thread if you would post the diagnostics that were printed by the shell that explains why it didn't work.

In this case, using correct syntax would seem to fix your problem:
Code:
ls *.geno | while read FN
do      awk '
                NR==FNR{A[$2]=$0; next}
                $1 in A{print A[$1], $0}
        ' unlocol_accessions "$FN" > "${FN/geno/geno2}"
done

or, if you insist on single line code instead of readable code:
Code:
ls *.geno | while read FN;do awk 'NR==FNR{A[$2]=$0; next} $1 in A{print A[$1], $0}' unlocol_accessions "$FN" > "${FN/geno/geno2}"; done

Or, more simply:
Code:
for FN in *.geno
do      awk '
                NR==FNR{A[$2]=$0; next}
                $1 in A{print A[$1], $0}
        ' unlocol_accessions "$FN" > "${FN/geno/geno2}"
done

Last edited by Don Cragun; 04-23-2015 at 04:14 PM.. Reason: Add alternative without pipeline and add quotes.
# 11  
Old 04-24-2015
As I tried to merge the second column of the file1 with first column of file2, I was able to run the command perfectly but I have a problem here. My file1 have 11580 id and file2 have 1805 id. the file2 is the original file and I want to merge file2 with file1 but instead I get 11580 id in my merge file, I will get 1613 common id in my merge file. I need to note in file1, I have id's which repeated more than one time. Does anyone have a suggestion for my problem?
# 12  
Old 04-24-2015
You lost me.

Please show us a sample set of representative input files and the output (or outputs) that should be produced from those input files.
# 13  
Old 04-24-2015
This is file1 (11580 id)
Code:
gi|358468608|ref|NW_003780270.1| 3935 T C 0 1 1
gi|358468608|ref|NW_003780270.1| 4071 C T 0 1 1
gi|358468608|ref|NW_003780270.1| 4110 C T 0 1 1
gi|358468608|ref|NW_003780270.1| 4377 C G 1 1 2
gi|358468608|ref|NW_003780270.1| 4387 C A 0 1 1
gi|358468608|ref|NW_003780270.1| 4476 A G 1 1 2
gi|358468610|ref|NW_003780268.1| 2707 G A 0 1 1
gi|358468610|ref|NW_003780268.1| 3290 C T 0 1 1
gi|358468610|ref|NW_003780268.1| 5909 A G 0 1 1
gi|358468610|ref|NW_003780268.1| 5950 G A 0 1 1
gi|358468610|ref|NW_003780268.1| 6085 T A 0 1 1
gi|358468624|ref|NW_003780254.1| 392 T C 1 1 2
gi|358468624|ref|NW_003780254.1| 600 A G 0 1 1
gi|358468624|ref|NW_003780254.1| 924 C T 0 1 1
gi|358468624|ref|NW_003780254.1| 972 A G 0 1 1
gi|358468629|ref|NW_003780249.1| 681 A C 0 1 1
gi|358468631|ref|NW_003780247.1| 138 A G 1 1 2
gi|358468631|ref|NW_003780247.1| 327 T G 0 1 1
gi|358468631|ref|NW_003780247.1| 511 A T 0 1 1
gi|358468631|ref|NW_003780247.1| 513 C G 0 1 1
gi|358468633|ref|NW_003780245.1| 1076 T C 0 1 1
gi|358468633|ref|NW_003780245.1| 348 T C 0 1 1
gi|358468633|ref|NW_003780245.1| 460 A G 1 1 2
gi|358468633|ref|NW_003780245.1| 591 G C 0 1 1
.
.
.
gi|358484429|ref|NW_003764465.1| 927 T G 0 1 1
gi|358484430|ref|NW_003764464.1| 366 G A 1 1 2
gi|358484430|ref|NW_003764464.1| 662 C G 0 1 1
gi|358484430|ref|NW_003764464.1| 664 C G 0 1 1
gi|358484430|ref|NW_003764464.1| 709 A G 0 1 1
gi|358484430|ref|NW_003764464.1| 782 T C 0 1 1
gi|358484431|ref|NW_003764463.1| 1295 A G 1 1 2
gi|358484431|ref|NW_003764463.1| 1868 G A 0 1 1
gi|358484431|ref|NW_003764463.1| 1921 G A 0 1 1
gi|358484431|ref|NW_003764463.1| 1980 A G 0 1 1
gi|358484431|ref|NW_003764463.1| 2003 T C 1 1 2
gi|358484431|ref|NW_003764463.1| 3595 T C 0 1 1
gi|358484431|ref|NW_003764463.1| 607 A G 0 1 1
gi|358484431|ref|NW_003764463.1| 686 C G 0 1 1
gi|358484431|ref|NW_003764463.1| 844 C G 0 1 1
gi|358484432|ref|NW_003764462.1| 541 A G 0 1 1
gi|358484451|ref|NW_003764443.1| 1126 G A 0 1 1
gi|358484451|ref|NW_003764443.1| 988 T C 0 1 1
gi|358484469|ref|NW_003764425.1| 785 G T 0 1 1
gi|358484470|ref|NW_003764424.1| 440 C T 1 1 2
gi|358484470|ref|NW_003764424.1| 735 T A 0 1 1
gi|358484471|ref|NW_003764423.1| 551 G T 1 1 2
gi|358484498|ref|NW_003764396.1| 2503 A G 0 1 1
gi|358484498|ref|NW_003764396.1| 381 A G 1 1 2
gi|358484513|ref|NW_003764381.1| 1351 T C 0 1 1

This is file2 (1805 id)
Code:
1       gi|358484521|ref|NW_003764373.1|
1       gi|358484520|ref|NW_003764374.1|
1       gi|358484519|ref|NW_003764375.1|
1       gi|358484518|ref|NW_003764376.1|
1       gi|358484517|ref|NW_003764377.1|
1       gi|358484516|ref|NW_003764378.1|
1       gi|358484515|ref|NW_003764379.1|
1       gi|358484514|ref|NW_003764380.1|
1       gi|358484513|ref|NW_003764381.1|
1       gi|358484512|ref|NW_003764382.1|
1       gi|358484511|ref|NW_003764383.1|
1       gi|358484510|ref|NW_003764384.1|
1       gi|358484509|ref|NW_003764385.1|
1       gi|358484508|ref|NW_003764386.1|
1       gi|358484507|ref|NW_003764387.1|
1       gi|358484506|ref|NW_003764388.1|
1       gi|358484505|ref|NW_003764389.1|
1       gi|358484504|ref|NW_003764390.1|
1       gi|358484503|ref|NW_003764391.1|
1       gi|358484502|ref|NW_003764392.1|
1       gi|358484501|ref|NW_003764393.1|
1       gi|358484500|ref|NW_003764394.1|
1       gi|358484499|ref|NW_003764395.1|
1       gi|358484498|ref|NW_003764396.1|
1       gi|358484497|ref|NW_003764397.1|
1       gi|358484496|ref|NW_003764398.1|
. 
.
.
LGE64   gi|358482732|ref|NW_003766162.1|
LGE64   gi|358482731|ref|NW_003766163.1|
LGE64   gi|358482730|ref|NW_003766164.1|
LGE64   gi|358482729|ref|NW_003766165.1|
LGE64   gi|358482728|ref|NW_003766166.1|
LGE64   gi|358482727|ref|NW_003766167.1|
LGE64   gi|358482726|ref|NW_003766168.1|
LGE64   gi|358482725|ref|NW_003766169.1|
LGE64   gi|358482724|ref|NW_003766170.1|
LGE64   gi|358482723|ref|NW_003766171.1|
LGE64   gi|358482722|ref|NW_003766172.1|
LGE64   gi|358482721|ref|NW_003766173.1|
LGE64   gi|358482720|ref|NW_003766174.1|
LGE64   gi|358482719|ref|NW_003766175.1|
LGE64   gi|358482718|ref|NW_003766176.1|
LGE64   gi|358482717|ref|NW_003766177.1|

Now, my original file is file2. I want to bring 2 column of file2 in front of file1. Notice that file1 have repeated id in its file.
# 14  
Old 04-24-2015
This was vice versa in post #1. Looking at these files, there's no match between file1's field 2 and file2's field one.

Please exercise way more care when specfying your problem.
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