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Problem to grep contents from a file

 
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# 1  
Old 04-06-2016
Problem to grep contents from a file
hi,

I'm trying to grep content from one file in another file.

The file that I'm searching into is large and hence I need to temporarily unzip it first.

Code:
gzip -dc ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz | grep '169997024\|190670539\|128051369' > 1000G_chrom2.txt

The command above worked and I get lines matching my grep content but I have a huge list to look into so I tried command below but it did not give any matching result . The text file contains exactly what I used above to write manually, so in theory the command below should produce the same result as command above. So I'm not sure why it doesn't produce matching lines and how could I modify the command?

Code:
 gzip -dc ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz | grep -f HIGH_conf_chrom2.txt > 1000G_chrom2.txt


This is how HIGH_conf_chrom2.txt look like
169997024
190670539
128051369
Last edited by janshamsani; 04-06-2016 at 04:40 AM..
# 2  
Old 04-06-2016
Assuming you want to know why "it didn't work"...

WHAT doesn't work? What does "HIGH_conf_chrom2.txt" look like?
# 3  
Old 04-06-2016
Perhaps explicitly state that you want to grep against STDIN...

Code:
 gzip -dc ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz | grep -f HIGH_conf_chrom2.txt - > 1000G_chrom2.txt

 
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