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Top Forums Shell Programming and Scripting Substitute newline with tab at designated field separator Post 302788985 by hanson44 on Tuesday 2nd of April 2013 09:55:28 PM
Old 04-02-2013
For sed, each N appends the next line to the pattern space. At the end of the script, sed prints out the four lines glommed together, with tab subsituted for newline:
Code:
$ sed "N; N; N; s/\n/\t/g" infile.fq
@GAIIX-300      ATAGTCAAAT      +       _SZS^\\\cd
@GAIIX-300      CATACGACAT      +       hhghfdffhh
@GAIIX-300      GACGACGTAT      +       gggfc[hh]f

Using the diagnostic l command, and turning off auto-print, makes it more clear what is going on:
Code:
$ sed -n "N; N; N; l; s/\n/\t/g" infile.fq
@GAIIX-300\nATAGTCAAAT\n+\n_SZS^\\\\\\cd$
@GAIIX-300\nCATACGACAT\n+\nhhghfdffhh$
@GAIIX-300\nGACGACGTAT\n+\ngggfc[hh]f$

I totally don't understand your tr example, would forget about using tr for this.
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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -jn m Join on the mth field of file n. If n is missing, use the mth field in each file. -o list Each output line comprises the fields specified in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. 7th Edition April 29, 1985 JOIN(1)
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