Public snipts » ssaha

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∞ filter the SSAHA2 result

#to filter the SSAHA2 result like
#===================================================
#Matches For Query 20489 (913 bases): b201.1e11.f.b1
#===================================================
#Score     Q_Name             S_Name            Q_Start    Q_End  #S_Start    S_End Direction #Bases identity
#ALIGNMENT::00 730   b201.1e11.f.b1 SC02       15      816    288648    #289465   F     802 97.51 913
#ALIGNMENT::00 730   b201.1e11.f.b1 SC05       15      816     34214     #35031   F     802 97.51 913

cat '/megx/home/shuang/result/ANME_vs_ANME1_SSAHA2/ANME_vs_ANME1_Endseq.txt' | egrep "ALIGNMENT" | sed 's/::/:/g' | sed 's/ \+/:/g' | cut -d: -f4,12

bash

#to filter the SSAHA2 result like
#===================================================
#Matches For Query 20489 (913 bases): b201.1e11.f.b1
#===================================================
#Score     Q_Name             S_Name            Q_Start    Q_End  #S_Start    S_End Direction #Bases identity
#ALIGNMENT::00 730   b201.1e11.f.b1 SC02       15      816    288648    #289465   F     802 97.51 913
#ALIGNMENT::00 730   b201.1e11.f.b1 SC05       15      816     34214     #35031   F     802 97.51 913

cat '/megx/home/shuang/result/ANME_vs_ANME1_SSAHA2/ANME_vs_ANME1_Endseq.txt' | egrep "ALIGNMENT" | sed 's/::/:/g' | sed 's/ \+/:/g' | cut -d: -f4,12

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posted by dgg32 on Jan 04, 2010 at 5:10 a.m. EST

A good read

MySQL in a Nutshell

Public snipts » ssaha

A good read

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