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Posted on 2012-04-05
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Last Modified: 2012-06-15
Hi,

I have two scripts:- pipeline.sh and fastacutter.pl

These are scripts which are pre-made and therefore I'm trying to modify.

There is a section in pipeline.sh which uses a program called formatdb:

#Formatdb
echo formatdb host and controls ...
$BLASTBIN/formatdb -i $PROTEOMEDIR/$HOST.fasta
$BLASTBIN/formatdb -i $PROTEOMEDIR/$CONTROL1.fasta
$BLASTBIN/formatdb -i $PROTEOMEDIR/$CONTROL2.fasta
$BLASTBIN/formatdb -i $PROTEOMEDIR/$CONTROL3.fasta
$BLASTBIN/formatdb -i $PROTEOMEDIR/$CONTROL4.fasta
$BLASTBIN/formatdb -i $PROTEOMEDIR/$CONTROL5.fasta

Basically, I don't need to do this, as I already have the results from the above code stored in a folder called 'database' found at:

/fs/nas15/home/mqbpgsm4/permanalysis/database

So essentially what I'm trying to do is remove the above code, and instead, whenever HOST, CONTROL1, CONTROL2, CONTROL3, CONTROL4 or CONTROL 5 are needed by pipeline.sh or fastacutter.pl, direct the script to /fs/nas15/home/mqbpgsm4/permanalysis/database to pick up the relevant file.

Any advice would be very much appreciated.

Thanks,

Stephen.
pipeline.sh
fastacutter.txt
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Question by:StephenMcGowan
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7 Comments
 
LVL 35

Expert Comment

by:Duncan Roe
ID: 37814716
How often would you run these scripts and how long does the bit you are trying to remove take? I would strongly urge that you not mess with them - it could easily lead to support issues down the track. In Breif:

If you need to ask, you shouldn't do it.
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LVL 51

Expert Comment

by:ahoffmann
ID: 37815141
> .. direct the script to  ..
what does this mean? can you please give an example
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LVL 40

Expert Comment

by:noci
ID: 37815237
Would it be wise to strip the appearant creation of an empty database out of the middle of a script?

Do you want to merge the results of 2 consecutive runs?
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WordPress Tutorial 2: Terminology

An important part of learning any new piece of software is understanding the terminology it uses. Thankfully WordPress uses fairly simple names for everything that make it easy to start using the software.

 
LVL 29

Expert Comment

by:Jan Springer
ID: 37815962
Please post an example of the 'database' file.  If I understand correctly, you want to read in the values from this file to be used in pipeline.sh instead of it calling formatdb.

If it isn't obvious what lines are for what variables, please let us know.
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Accepted Solution

by:
serialband earned 500 total points
ID: 37816835
It seems that you just have to comment out the lines you've listed and change the PROTEOMEDIR assignment in line 55 and line 140 to match the directory you need.
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Author Comment

by:StephenMcGowan
ID: 37932458
I've requested that this question be deleted for the following reason:

Abandoned
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