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# 1  
Old 11-08-2012
Merge with common column
hi i have two files and i wanted to join them using common column. try to do this using "join" command but that did not help.

File 1:

Code:
123             9a.vcf               hy92.vcf          hy90.vcf
Index    Ref     Alt     Ref     Alt     Ref     Alt
315       14       0       7       4      17       2
321        5       9       3       8       7      11
327       13       0       9       3      16       1
336       13       1       8       4      18       1
445       14       0       9       3      18       1

file 2:
Code:
Gene     Position         Reference Base         Alternate Base          Alternate count         Alternate count         Snp format      Sequence
lcl|utg7180000001423     315      A      G      3                [A/G]   CTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTTAAACTCCAAAACATATATCTACTTCAAAGTAGTGTTTTCCTGAGAGAAAGCACTATCGATAAGTTATGTCCCAACTCCAAATTATTACATCAAAGTAGAAACAAGATGACATATATATATCAACCGTATATTCTGCACATGATGTG
lcl|utg7180000001423     321      G      A/A,C  41       39,2    [-/-]   CTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTTAAACTCCAAAACATATATCTACTTCAAAGTAGTGTTTTCCTGAGAGAAAGCACTATCGATAAGTTATGTCCCAACTCCAAATTATTACATCAAAGTAGAAACAAGATGACATATATATATCAACCGTATATTCTGCACATGATGTG
lcl|utg7180000001423     327      A      C      4                [A/C]   CTAGAATCACTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTTAAACTCCAAAACATATATCTACTTCAAAGTAGTGTTTTCCTGAGAGAAAGCACTATCGATAAGTTATGTCCCAACTCCAAATTATTACATCAAAGTAGAAACAAGATGACATATATATATCAACCGTATATTCTGCACATGATGTG

i wanted to match first column in 1st file with 2nd column in second file and get union of both files i.e i need all the fields from file 1 as well as file 2.

---------- Post updated at 12:44 AM ---------- Previous update was at 12:21 AM ----------

an update is that the following code is able to merge the columns but its taking off the headings. i need to retain them in the final file..

Code:
#!/bin/awk -f
  # store the first file, indexed by col2
  NR==FNR {f1[$1] = $0; next}
  # output only if file1 contains file2's col2
  ($2 in f1) {print $0,"\t",f1[$2]}

Last edited by Scrutinizer; 11-08-2012 at 01:44 AM.. Reason: Changed icode to code
# 2  
Old 11-08-2012
If you are using join then the files need to be in sorted order and the headers would need to be removed... What should the output look like (sample)?


--edit--
Try:
Code:
#!/bin/awk -f
  # store the first file, indexed by col2
  NR==FNR {f1[$1] = $0; next}
  # output only if file1 contains file2's col2  
  $2 in f1{$0=$0 "\t" f1[$2]}
  {print}

Last edited by Scrutinizer; 11-08-2012 at 01:57 AM..
# 3  
Old 11-08-2012
Thank you but this is giving out the headings for second file only. i want those for first file also. First file contains headings in two rows. Also this script is printing out common column twice.. it need to be printed only once.
# 4  
Old 11-08-2012
Try

Code:
awk 'NR<3{print}
  NR==FNR {f1[$1]=$0;next}
  $2 in f1{$0=$0 "\t" f1[$2]}
  {print}' file1 file2

# 5  
Old 11-08-2012
Thankyou , pamu

but its printing the headers in three lines on one file and no headers on other file. see the output below.

Code:
123             9a.vcf               hy92.vcf          hy90.vcf
Index    Ref     Alt     Ref     Alt     Ref     Alt
Gene     Position         Reference Base         Alternate Base          Alternate count         Alternate count         Snp format      Sequence
lcl|utg7180000001423     315      A      G      3                [A/G]   CTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTTAAACTCCAAAACATATATCTACTTCAAAGTAGTGTTTTCCTGAGAGAAAGCACTATCGATAAGTTATGTCCCAACTCCAAATTATTACATCAAAGTAGAAACAAGATGACATATATATATCAACCGTATATTCTGCACATGATGTG      315       14       0       7       4      17       2
lcl|utg7180000001423     321      G      A/A,C  41       39,2    [-/-]   CTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTTAAACTCCAAAACATATATCTACTTCAAAGTAGTGTTTTCCTGAGAGAAAGCACTATCGATAAGTTATGTCCCAACTCCAAATTATTACATCAAAGTAGAAACAAGATGACATATATATATCAACCGTATATTCTGCACATGATGTG      321        5       9       3       8       7      11
lcl|utg7180000001423     327      A      C      4                [A/C]   CTAGAATCACTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTTAAACTCCAAAACATATATCTACTTCAAAGTAGTGTTTTCCTGAGAGAAAGCACTATCGATAAGTTATGTCCCAACTCCAAATTATTACATCAAAGTAGAAACAAGATGACATATATATATCAACCGTATATTCTGCACATGATGTG     327       13       0       9       3      16       1

# 6  
Old 11-08-2012
Quote:
Originally Posted by empyrean
Thankyou , pamu

but its printing the headers in three lines on one file and no headers on other file. see the output below.
try

Code:
awk 'NR<3{s=s?s" "$0:$0}
  NR==FNR {f1[$1]=$0;next}
  FNR==1 && s{print $0,s;s=""}
  $2 in f1{print $0"\t"f1[$2]}' file1 file2

# 7  
Old 11-08-2012
Thanks again. But the delimiters are not aligning i mean the heading is not in tab delimited format as the results are.. another thing is that the common column is repeating twice. i want it to be in second column but shoudnt repeat after sequence info.
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