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Add a new column to txt file containing filename

 
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# 1  
Old 03-21-2012
Add a new column to txt file containing filename
I would like help adding a new column to a large txt file (~10MB) that contains the filename. I have searched other posts but have not found an adequate solution.

I need this extra column so I can concatenate >100 files and perform awk searches on this large file.

My current txt file look like this

Code:
#chr_name       chr_start       chr_end ref_base        alt_base        hom_het snp_quality     tot_depth       alt_depth       region  gene    change  annotation      dbSNP135_full   dbSNP135_common 1000G_2010Nov_allele_freq       1000G_2011Oct_allele_freq       SCS     CLN     OMIM
chr01   14542   14542   A       G       hom     4.11    3       3       ncRNA_exonic    WASH7P  .       .       rs1045833       .       .       .       .       .       .
chr01   14574   14574   A       G       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs28503599      .       .       .       .       .       .
chr01   14590   14590   G       A       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs707679        .       .       .       .       .       .
chr01   14599   14599   T       A       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs707680        .       .       .       .       .       .
chr01   14604   14604   A       G       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs4021621       .       .       .       .       .       .
chr01   14610   14610   T       C       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs79134172      .       .       .       .       .       .
chr01   14699   14699   C       G       het     3.54    11      3       ncRNA_exonic    WASH7P  .       .       rs11490464      .       0.02    .       .       .       .
chr01   14907   14907   A       G       hom     184     28      27      ncRNA_intronic  WASH7P  .       .       rs6682375       .       .       .       .       .       .
chr01   14930   14930   A       G       hom     207     45      42      ncRNA_intronic  WASH7P  .       .       rs6682385       rs75454623      0.71    .       .       .       .
chr01   14933   14933   G       A       het     113     46      21      ncRNA_intronic  WASH7P  .       .       .       .       0.057   .       .       .       .
chr01   14976   14976   G       A       het     140     47      20      ncRNA_exonic    WASH7P  .       .       rs71252251      .       .       .       .       .       .
chr01   15118   15118   A       G       het     17.4    8       5       ncRNA_intronic  WASH7P  .       .       rs11580262      .       0.041   .       .       .       .
chr01   17701   17701   C       T       het     30      23      9       ncRNA_exonic    WASH7P  .       .       .       .       .       .       .       .       .
chr01   662857  662857  G       A       hom     87      36      32      ncRNA_exonic    LOC100133331    .       .       rs6689091       .       .       .       .       .       .
chr01   663097  663097  G       C       hom     120     91      85      ncRNA_exonic    LOC100133331    .       .       rs61769340      .       0.67    .       .       .       .
chr01   761732  761732  C       T       hom     222     45      45      ncRNA_exonic    LINC00115       .       .       rs2286139       rs2286139       0.537   0.61    .       .       .
chr01   761752  761752  C       T       hom     222     26      23      ncRNA_exonic    LINC00115       .       .       rs1057213       rs1057213       0.544   0.75    .       .       .
chr01   761800  761800  A       T       hom     22      5       3       ncRNA_exonic    LINC00115       .       .       rs1064272       .       0.114   .       .       .       .
chr01   761811  761811  G       A       hom     33.5    4       4       ncRNA_exonic    LINC00115       .       .       rs1057212       .       0.59    .       .       .       .
chr01   762273  762273  G       A       hom     190     52      48      ncRNA_exonic    LINC00115       .       .       rs3115849       rs3115849       0.555   0.72    .       .       .
chr01   762589  762589  G       C       hom     207     58      53      ncRNA_exonic    LINC00115       .       .       rs3115848       rs71507461      0.73    0.72    .       .       .
chr01   762592  762592  C       G       hom     180     60      53      ncRNA_exonic    LINC00115       .       .       rs3131950       rs71507462      0.72    0.72    .       .       .
chr01   762601  762601  T       C       hom     222     60      59      ncRNA_exonic    LINC00115       .       .       rs3131949       rs71507463      0.72    0.72    .       .       .
chr01   762632  762632  T       A       hom     222     89      87      ncRNA_exonic    LINC00115       .       .       rs3131948       rs61768173      0.71    0.72    .       .       .
chr01   787262  787262  C       G       hom     87      10      10      ncRNA_intronic  LOC643837       .       .       rs2905056       rs56108613      0.668   0.78    .       .       .

I would like to add a new column (at either the start or end, but start is preferred) that contains the filename in each line.

This is what I would like the output to look like for filename=samplexxx.txt

Code:
samplexxx #chr_name       chr_start       chr_end ref_base        alt_base        hom_het snp_quality     tot_depth       alt_depth       region  gene    change  annotation      dbSNP135_full   dbSNP135_common 1000G_2010Nov_allele_freq       1000G_2011Oct_allele_freq       SCS     CLN     OMIM
samplexxx chr01   14542   14542   A       G       hom     4.11    3       3       ncRNA_exonic    WASH7P  .       .       rs1045833       .       .       .       .       .       .
samplexxx chr01   14574   14574   A       G       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs28503599      .       .       .       .       .       .
samplexxx chr01   14590   14590   G       A       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs707679        .       .       .       .       .       .
samplexxx chr01   14599   14599   T       A       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs707680        .       .       .       .       .       .
samplexxx chr01   14604   14604   A       G       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs4021621       .       .       .       .       .       .
samplexxx chr01   14610   14610   T       C       hom     20.2    6       6       ncRNA_exonic    WASH7P  .       .       rs79134172      .       .       .       .       .       .

I have >100 files that I need to do this for, so any help will be greatly appreciated. I have no desire to open each file manually in excel to do this!

Many thanks Smilie
# 2  
Old 03-22-2012
Try with some two files, and check the output and then apply it for all the files.

Code:
 
for i in *; do nawk '{print FILENAME"\t"$0}' $i > $i.bk; mv $i.k $i; done

This User Gave Thanks to itkamaraj For This Post:
kellywilliams
# 3  
Old 03-22-2012
Hi there.
Maybe you should use sed.
Try doing something like:

Code:
sed -i.bkp 's/^/filenameU/' your_input_file.txt

Is your columns delimited by tab or spaces?
In case of tabs, and, if you're using bash, just replace the U character mentioned aboved by Ctrl-V then the TAB key. This will let you get the TAB you need.
That's it. Hope it helps.
This User Gave Thanks to chapeupreto For This Post:
kellywilliams
# 4  
Old 03-25-2012
Quote:
Originally Posted by itkamaraj
Try with some two files, and check the output and then apply it for all the files.

Code:
 
for i in *; do nawk '{print FILENAME"\t"$0}' $i > $i.bk; mv $i.k $i; done

Worked perfectly, just need to change
Code:
mv $i.k $i

to
Code:
mv $i.bk $i

and it was great. Thank you
# 5  
Old 03-26-2012
Add a new column to txt file containing filename
Hi Kelly,

Try this too,

Code:
nawk '{a=FILENAME;}{print a"\t"$0}' yourFilename > yourFilename.bk && mv yourFilename.bk yourFilename

since you are working for single file, you can get your expected output in single command itself.

Regards,
SHANMU
 
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