What do you mean, this is a better example of the data? Your script has three input files: list.txt, code_to_value.txt, and table_values.txt. Is this example of the data an example of one of these input files? Is it an example of the output you're trying to produce?
From your sample code, we can see that there are several things that could be made more efficient; but without knowing what you're trying to do, we can easily produce efficient code that doesn't do anything at all like what you want to do. Why do you have a loop, if you only want to keep the output produced by the last time through the loop?
Please help us help you. Show us sample data for each of your three input files. And, given those sample input files, what output are you trying to produce in test.output?
This User Gave Thanks to Don Cragun For This Post:
code_to_value.txt ## Table for decoding table_values.txt (not in the same order of table_values.txt)
Code:
PT_0000000001 A G
PT_0000000002 G T
PT_0000000004 A C
PT_0000000003 C G
So, I want to go line per line of table_values.txt and replace 1, 2 or 3 buy the combination of alleles on code_to_value.txt.
The code is: 1 means 2 x first allele (second column), 2 means second column + third column, 3 means 2x third column (for each PT_*)
For exemple, for PT_0000000001 1 means AA, 2 AG and 3 GG. While for PT_0000000002 1 means GG, 2 GT and 3 TT.
So the final output I am trying is:
Code:
PT_0000000001 AA AG AA AA AA AA AG AG AA AA AG
PT_0000000002 GG GT TT GG GT TT GT GT GG TT GG
PT_0000000003 GG CG GG CG GG GG CG CC CC CG GG
PT_0000000004 AC AC AA AC CC AA CC AC AA AA AC
Since your code_to_value.txt file only contains 17 characters per line (not counting the terminating <newline> character), the cut calls creating the files value_1 and value_2 always produce empty files. So, even if the calls to paste work, the files code_1, code_2, and code_3 will also always be empty files.
When I run your code on OS X, I get errors from all of your invocations of paste instead of errors from sed. Bur rather than invoking cat nine times, cut, grep, and paste twelve times, and sed four times; the following script using a single invocation of awk seems to do what you said you wanted done (without using the file list.txt).
With your sample code_to_value.txt and table_values.txt input files, it produces the output:
Code:
PT_0000000001 AA AA AA AA AA AA AG AG AA AA AG
PT_0000000002 GT GT TT GG GT TT GT GT GG TT GG
PT_0000000003 GG CG GG CG GG GG CG CC CC CG GG
PT_0000000004 CC AC AA AC CC AA CC AC AA AA AC
rather than the output you said you wanted:
Code:
PT_0000000001 AA AG AA AA AA AA AG AG AA AA AG
PT_0000000002 GG GT TT GG GT TT GT GT GG TT GG
PT_0000000003 GG CG GG CG GG GG CG CC CC CG GG
PT_0000000004 AC AC AA AC CC AA CC AC AA AA AC
If I understand your requirements correctly, I believe the output shown in red in the output you said you were trying to get is inconsistent with your requirements.
Note that if you input files have Windows <carriage-return><line-feed> line terminators instead of UNIX and Linux <newline> line terminators, you'll need to change the line:
Code:
awk '
in the above script to something like:
Code:
awk '
{ gsub(/\r/, "")
}
to get rid of the extraneous <carriage-return> characters.
I hope this helps.
This User Gave Thanks to Don Cragun For This Post:
Greetings!
Have a quick question for the community today; this time looking at a nifty little sed puzzle ;)
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12-18-2014
