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Top Forums Shell Programming and Scripting Grep two files: -F flag gives weird output Post 303007366 by genome on Wednesday 15th of November 2017 05:02:26 PM
Old 11-15-2017
Grep two files: -F flag gives weird output

Hi Members,

I'm confused with grep -F option. Goal is to get all the lines from file2 that have exact gene name from gene list (file one).

File one has list of genes:
Quote:
CR1
PSEN2
GYPC
BIN1
CYP27C1
ERCC3
MAP3K2
PROC
MIR4783
IWS1
File two has lot more information pertinent to genes in file one:
Quote:
19 19256812 19256812 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV
19 19257646 19257646 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV
I use three following commands:

1)
Code:
grep -wf gene file2

Not output. This is expected.

2)
Code:
 grep -Ff gene file2

This gives me both the lines in file2:

Quote:
19 19256812 19256812 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV
19 19257646 19257646 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV
However, there's no gene as MEF2B or MEF2BNB-MEF2B in gene list.

But gene MEF2C is present in gene list.

That means -F options collects anything. Am I understanding this correctly?

3)
Code:
 grep -Fxf gene file2

No output
I guess x looks per line basis

4)

Code:
grep -Fwf gene file2

This matches with grep -wf gene file2

I'm confused which is correct way to get appropriate answer. Data is humongous so I'd not know where I made mistake.

Command one and four look good to go.

Would appreciate any help here.

Last edited by genome; 11-15-2017 at 06:11 PM.. Reason: added fourth command
 

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GO::Model::GeneProduct(3pm)				User Contributed Perl Documentation			       GO::Model::GeneProduct(3pm)

NAME
GO::Model::GeneProduct - gene product in a particular species DESCRIPTION
represents a gene product in a particular species (this will effectively always be refered to implicitly by the gene symbol even though a gene may have >1 product) acc Usage - Returns - Args - symbol Usage - Returns - Args - type Usage - Returns - Args - full_name Usage - Returns - Args - as_str Usage - Returns - Args - add_synonym synonym_list accessor: gets/set list of synonyms [array reference] speciesdb Usage - Returns - Args - add_seq Usage - Returns - Args - GO::Model::Seq seq_list Usage - Returns - GO::Model::Seq listref Args - seq Usage - Returns - GO::Model::Seq Args - returns representative sequence object for this product properties Usage - Returns - hashref Args - hashref set_property Usage - $sf->set_property("wibble", "on"); Returns - Args - property key, property scalar note: the property is assumed to be multivalued, therefore $sf->set_property($k, $scalar) will add to the array, and $sf->set_property($k, $arrayref) will set the array get_property Usage - Returns - first element of the property Args - property key get_property_list Usage - Returns - the property arrayref Args - property key to_fasta Usage - Returns - Args - returns the longest seq by default perl v5.14.2 2013-02-07 GO::Model::GeneProduct(3pm)
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