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Top Forums Programming Run sed and awk in multiple files in adirectory Post 303018347 by MadeInGermany on Monday 4th of June 2018 11:15:31 AM
Old 06-04-2018
Proposal: a bash script with a for loop
Code:
#!/bin/bash
fmask="ERR598955_orfm.fna"
for f in $fmask.*
do
  [ -f "$f" ] || continue # ensure this is an existing file
  ext=${f#$fmask} # strip off the leading fmask
  pattern=$(awk '{print $1; exit}' "$f") # pattern is the 1st word in the 1st line
  sed -n '1,/^'"${pattern}"'$/ d ; /^>/,$ p' "$f" > "first_out.$ext"
done

You might need to work on it...
This User Gave Thanks to MadeInGermany For This Post:
 

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GREP(1) 						      General Commands Manual							   GREP(1)

NAME
grep, g - search a file for a pattern SYNOPSIS
grep [ option ... ] pattern [ file ... ] g [ option ... ] pattern [ file ... ] DESCRIPTION
Grep searches the input files (standard input default) for lines that match the pattern, a regular expression as defined in regexp(7) with the addition of a newline character as an alternative (substitute for |) with lowest precedence. Normally, each line matching the pattern is `selected', and each selected line is copied to the standard output. The options are -c Print only a count of matching lines. -h Do not print file name tags (headers) with output lines. -e The following argument is taken as a pattern. This option makes it easy to specify patterns that might confuse argument parsing, such as -n. -i Ignore alphabetic case distinctions. The implementation folds into lower case all letters in the pattern and input before interpre- tation. Matched lines are printed in their original form. -l (ell) Print the names of files with selected lines; don't print the lines. -L Print the names of files with no selected lines; the converse of -l. -n Mark each printed line with its line number counted in its file. -s Produce no output, but return status. -v Reverse: print lines that do not match the pattern. -f The pattern argument is the name of a file containing regular expressions one per line. -b Don't buffer the output: write each output line as soon as it is discovered. Output lines are tagged by file name when there is more than one input file. (To force this tagging, include /dev/null as a file name argument.) Care should be taken when using the shell metacharacters $*[^|()= and newline in pattern; it is safest to enclose the entire expression in single quotes '...'. An expression starting with '*' will treat the rest of the expression as literal characters. G invokes grep with -n and forces tagging of output lines by file name. If no files are listed, it searches all files matching *.C *.b *.c *.h *.m *.cc *.java *.cgi *.pl *.py *.tex *.ms SOURCE
/src/cmd/grep /bin/g SEE ALSO
ed(1), awk(1), sed(1), sam(1), regexp(7) DIAGNOSTICS
Exit status is null if any lines are selected, or non-null when no lines are selected or an error occurs. GREP(1)
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