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Top Forums Shell Programming and Scripting Grep two files: -F flag gives weird output Post 303007417 by genome on Thursday 16th of November 2017 09:22:52 AM
Old 11-16-2017
Quote:
Originally Posted by Don Cragun
What output do you get from the command:
Code:
grep -E 'MEF|SNV' gene

This gives me following output:
Code:
grep -E 'MEF|SNV' ext_gene_list.txt

Quote:
MEF2C
I'm on Unix:

x86_64 x86_64 x86_64 GNU/Linux

---------- Post updated at 09:22 AM ---------- Previous update was at 09:05 AM ----------

I'm unable to understand why I get output for:
Code:
grep -Ff ext_gene_list.txt no_idea.txt

Quote:
19 19256812 19256812 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV
19 19257646 19257646 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV
no_idea.txt is a tab sep file.

There's no gene with name: "exonic" "MEF2B" "MEF2BNB-MEF2B", "MEF2BNB" "nonsynonymous SNV", "SNV"

So if there's no gene, I should not get any output with the above command. Which baffles me with -F file. I'm not sure when to use -F flag.

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dlags2.f(3)							      LAPACK							       dlags2.f(3)

NAME
dlags2.f - SYNOPSIS
Functions/Subroutines subroutine dlags2 (UPPER, A1, A2, A3, B1, B2, B3, CSU, SNU, CSV, SNV, CSQ, SNQ) DLAGS2 Function/Subroutine Documentation subroutine dlags2 (logicalUPPER, double precisionA1, double precisionA2, double precisionA3, double precisionB1, double precisionB2, double precisionB3, double precisionCSU, double precisionSNU, double precisionCSV, double precisionSNV, double precisionCSQ, double precisionSNQ) DLAGS2 Purpose: DLAGS2 computes 2-by-2 orthogonal matrices U, V and Q, such that if ( UPPER ) then U**T *A*Q = U**T *( A1 A2 )*Q = ( x 0 ) ( 0 A3 ) ( x x ) and V**T*B*Q = V**T *( B1 B2 )*Q = ( x 0 ) ( 0 B3 ) ( x x ) or if ( .NOT.UPPER ) then U**T *A*Q = U**T *( A1 0 )*Q = ( x x ) ( A2 A3 ) ( 0 x ) and V**T*B*Q = V**T*( B1 0 )*Q = ( x x ) ( B2 B3 ) ( 0 x ) The rows of the transformed A and B are parallel, where U = ( CSU SNU ), V = ( CSV SNV ), Q = ( CSQ SNQ ) ( -SNU CSU ) ( -SNV CSV ) ( -SNQ CSQ ) Z**T denotes the transpose of Z. Parameters: UPPER UPPER is LOGICAL = .TRUE.: the input matrices A and B are upper triangular. = .FALSE.: the input matrices A and B are lower triangular. A1 A1 is DOUBLE PRECISION A2 A2 is DOUBLE PRECISION A3 A3 is DOUBLE PRECISION On entry, A1, A2 and A3 are elements of the input 2-by-2 upper (lower) triangular matrix A. B1 B1 is DOUBLE PRECISION B2 B2 is DOUBLE PRECISION B3 B3 is DOUBLE PRECISION On entry, B1, B2 and B3 are elements of the input 2-by-2 upper (lower) triangular matrix B. CSU CSU is DOUBLE PRECISION SNU SNU is DOUBLE PRECISION The desired orthogonal matrix U. CSV CSV is DOUBLE PRECISION SNV SNV is DOUBLE PRECISION The desired orthogonal matrix V. CSQ CSQ is DOUBLE PRECISION SNQ SNQ is DOUBLE PRECISION The desired orthogonal matrix Q. Author: Univ. of Tennessee Univ. of California Berkeley Univ. of Colorado Denver NAG Ltd. Date: November 2011 Definition at line 152 of file dlags2.f. Author Generated automatically by Doxygen for LAPACK from the source code. Version 3.4.1 Sun May 26 2013 dlags2.f(3)
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