Parse file lines, using multiple variables in bash loop

Question

Given a file with 2 columns, a string and a filename, how can these be looped with a grep command? Would also like to direct the output to same name as SEQFILE in different folder. Believe the following is close, with correct quoting missing:

while IFS=" ", read SEQID SEQFILE
do
grep -A1 -m 1 ${SEQID} ${SEQFILE} > ./tmp/${SEQFILE}
done < missingSeq.txt

Is the file comma or space delimited? Your IFS above would make me think either/both. — kojiro
– kojiro, Commented Jul 24, 2014 at 19:12
one thing is your ifs .. the second is your redirection operator > — shiv garg
– shiv garg, Commented Jul 24, 2014 at 19:14
Can you be sure that the second field is unique over the missingSeq.txt file? Because if it is not, later occurrences will overwrite earlier. — kojiro
– kojiro, Commented Jul 24, 2014 at 19:20

kojiro · Accepted Answer · 2014-07-24 19:16:30Z

2

If the file is comma delimited, then IFS=" ", makes no sense, but if it's whitespace delimited, then the comma is getting in the way. This is likely to solve the problem you present above:

while IFS=' ' read id file; do
    grep -A1 -m1 "$id" "$file" > "./tmp/$file"
done < missingSeq.txt

answered Jul 24, 2014 at 19:16

kojiro

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1 Comment

user2525172 Over a year ago

You're right it is whitespace, and the extra comma was the error. The two column file is an error report from a job run in parallel, and it is needed to append each SEQID (and following line) for each filename. Thanks!

Deleted User · Accepted Answer · 2014-07-24 19:52:21Z

0

IFS=' '
while read seq_id seq_file; do
   grep -A1 -m1 "$seq_id" "$seq_file" >> ./tep/seq_file    # i assume "tep" was actually meant
done < missingSeq.txt

edited Jul 24, 2014 at 19:52

Deleted User

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answered Jul 24, 2014 at 19:20

shiv garg

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2 Comments

shiv garg Over a year ago

do the little do it clean

shiv garg Over a year ago

>> will append to the file..while > will overwrite

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