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.
Not digging too deep, I can see that
- your single quoting of the sed commands is consistently wrong - the entire respective command needs to be quoted.
- the redirection into the to-be-modified file truncates it before anything is read from it, so I'm very surprised that only several files should be completely blank.
- running 7 seds (i.e. creating 7 processes) for 4000 file is resource hungry and may become somewhat slow.
- running a for loop from 0 to 4000 with i the loop variable, why do you use another j variable?
How about
Code:
for FN in clus*phy; do sed '/aver\|anid\|anig\|acar\|azon\|awen\|akaw/ s/_[^ ]*//' $FN > ${FN}.tmp; done
Move the .tmp files to the origial ones when happy.
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12-08-2017
