I want to replace 7 patterns (aver, anid, anig, acar, azon, awen, akaw) in all the files. The resulting file should be like (No change in file name)
Code:
$cat clus_grp_seq10_g.phy
18 1002
anig ATGGTTTCGCAGCGTGATAGAGAATTGTTTAGGGATGATATTCGCTCGCGAGGAACGAAGCTCAATGCTGCCGAGCGCGAGAGTCTGCTAAGGCCATATCTGCCAGATCCGTCTGACCTTCCACGCAGGCCACTTCAGCGGCGCAAGAAGGTTCCTCG
aver ATGGTTTCGCAACGAGAT---------AGAGAATTGAATATCACGGCTTCCTCAGGGGTCTCTGGCATTATGCTGGTGCTCAGATGAGGTTTGGC
anid ATGGTCTCACAGCGTGACAGAGAGTTGGCTGTTGAATACCAGGGCTATCTCAGGGGTTTGTGGCATTACGCTGGGGCCCAGATGCGATTTGGC
azon ATGGCCCTAGCACGTGATAGAGAATTACTGAGGGACACTATTCGCACCCAAGGGACCGCACTTACTGCTGCCGATCGCGAAAATATCCTGAAGCCATATCTGCCGGATCCATCAGAACTTGCACGTCGGCCACTACAGCGACAGAAGAAAGC
awen ATGGTATCACAACGGGATAGAGTGGTGTGTCTGCC------------------------------------------------CTCTACAGGTCA------AAACAGTGCGAAATA---------AA
acar ATGGCCCT
akaw ---------ATGGTCTCAC---------AGCGTGACAGAGAGT---------TGGCTGTTGAATACCAGGGCTATCTCAGGGGTTTGTGGCATTACGC
I wrote a bash script for this
Code:
#!/bin/bash
j=1
for ((i=0;i<=4000;i++));
do
echo "$j"
sed -e s/'aver_[^ ]*'/aver/g clus_grp_seq"$j"_g.phy | sed -e s/'anid_[^ ]*'/anid/g | sed -e s/'anig_[^ ]*'/anig/g | sed -e s/'acar_[^ ]*'/acar/g | sed -e s/'azon_[^ ]*'/azon/g | sed -e s/'awen_[^ ]*'/awen/g | sed -e s/'akaw_[^ ]*'/akaw/g -> clus_grp_seq"$j"_g.phy
wait
let j++
done
but the parser is making several files completely blank. In the folder some files like clus_grp_seq2000_g.phy does not exists, in such case blank file like clus_grp_seq2000_g.phy is OK. But in cases even the file exists in the folder like clus_grp_seq10_g.phy as shown above the parser is making blank files.
Please let me know the problem or suggest an alternative solution.
hi,
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Discussion started by: ncwxpanther
1 Replies
LEARN ABOUT MINIX
grep
GREP(1) General Commands Manual GREP(1)NAME
grep - search a file for lines containing a given pattern
SYNOPSIS
grep [-elnsv] pattern [file] ...
OPTIONS -e-e pattern is the same as pattern
-c Print a count of lines matched
-i Ignore case
-l Print file names, no lines
-n Print line numbers
-s Status only, no printed output
-v Select lines that do not match
EXAMPLES
grep mouse file # Find lines in file containing mouse
grep [0-9] file # Print lines containing a digit
DESCRIPTION
Grep searches one or more files (by default, stdin) and selects out all the lines that match the pattern. All the regular expressions
accepted by ed and mined are allowed. In addition, + can be used instead of * to mean 1 or more occurrences, ? can be used to mean 0 or 1
occurrences, and | can be used between two regular expressions to mean either one of them. Parentheses can be used for grouping. If a
match is found, exit status 0 is returned. If no match is found, exit status 1 is returned. If an error is detected, exit status 2 is
returned.
SEE ALSO cgrep(1), fgrep(1), sed(1), awk(9).
GREP(1)