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How to take out multiple matches in file2 using file1 as a reference?

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# 1  
Old 03-14-2012
How to take out multiple matches in file2 using file1 as a reference?
Hi guys,

As the title, I want to take out the lines in file2 if the TCONS_* matches that in file1. Then put the lines in a file3. The TCONS numbers ranges from TCONS_00000024 to TCONS_00381684. Those numbers are continuous in file2, not in file1. Below is just some lines of file1 and file2

File1:
Code:
TCONS_00000284        
TCONS_00198804
TCONS_00198826
TCONS_00067013


File2:

Code:
chr1   exon    65233257        65233407     transcript_id "TCONS_00000284"; 
chr1   exon    65236893        65237073     transcript_id "TCONS_00000284"; 
chr1   exon    65233257        65233407     transcript_id "TCONS_00000285";
chr1   exon    65236893        65237073     transcript_id "TCONS_00000285";


Thanks very much!


Last edited by joeyg; 03-14-2012 at 03:48 PM.. Reason: Please use CodeTags for sample files and scripts
# 2  
Old 03-14-2012
Take a look at the command
Code:
grep -f

# 3  
Old 03-14-2012
Quote:
Originally Posted by joeyg
Take a look at the command
Code:
grep -f

Thanks Joey. But I need to compare all the transcript id in file1 and file2, so I need to use some loops. I'm quite new to perl, could you please give me more details about the codes?
# 4  
Old 03-14-2012
Why perl? grep -f is what you want

Code:
# this makes file3
grep -f file1 file2 > file3
# selectively lose lines in file2 that are in file1
grep -f -v file2 file2 > tmpfile
# read and check that tmpfile is correct.  then
mv tmpfile file2

You don't need perl or loops, joeyg gave you great advice.
# 5  
Old 03-14-2012
Quote:
Originally Posted by jim mcnamara
Why perl? grep -f is what you want

Code:
# this makes file3
grep -f file1 file2 > file3
# selectively lose lines in file2 that are in file1
grep -f -v file2 file2 > tmpfile
# read and check that tmpfile is correct.  then
mv tmpfile file2

You don't need perl or loops, joeyg gave you great advice.
Does the "grep -vf file1 file2>tmpfile" mean move the the lines in file2 that are not in file1 to tmpfile? I don't need those that don't match.
What does the the first line mean?
Thanks very much.
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