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Excellent! It looks like that does the job and outputs 9 result files.

Thanks!

Bob

Well that almost works. I did make a mistake in the input file. There are two more definitions that come up Bacterial:5S_rRNA and Eukaryotic:8S_rRNA. This leaves me to wonder whether there are...

I have an output file similar to this

>HWI-ST766:129:D0WJDACXX:4:2308:16645:199681.1 /start=1 /end=100 /strand=+ Eukaryotic18S_rRNA
GATTAAGCCATGCATGTGTAAGTTTAAAGTCCTAGAAGGATGAAACTGCGGACGGCTCAT...

Yes, the data lines would start with 0.1 in the second column. However I need this to work over files with different numbers of samples (more or less columns) and incorporate a filter to get rid of...

The display is indeed poor, is this better?

So for Prevotellaceae, D1 the result would be =923/3323
Xylanibacter sample D17 would be =41/4704


taxlevel rankID taxon ...

Hello Forumites.

You guys really helped me out in the past with manipulating some files with awk commands. Now, the output from the analysis program has changed and I would like to rework the...

Excellent. thank-you!

I am trying to update an older program on a small cluster. It uses individual files to send jobs to each node. However the newer database comes as one large file, containing over 10,000 records. I...

Many many thanks! You guys have saved me days of work!

That clued me in and I used

sed -d '/unclassified/d' result_B.txt > 1.txt


to get rid of the lines with unclassified.

The sort is still a problem. I can't seem to get the hierarchical...

When I used a real world result file I came up with a couple of other problems. The file now has the right data but the classification produces extraneous data in the form of duplicated...

After the great awk solution to my last problem (that saved me days of work) I thought I would try again.

I now have a result file that consists of two identifier columns and then columns of data...

I renamed my files to be sample1.txt sample2.txt (they were actually things like ONA.txt 125.txt OTS.txt 499.txt) and put them in a separate directory and then ran the command.
It worked nicely.
...

I have a number of result files (the number of files varies) that I need to combine into a new file with new columns for each data line. If one file does not have a result for any row it is set to...