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Inserting IDs from a text file into a sequence alignment file

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# 1  
Old 11-19-2014
Inserting IDs from a text file into a sequence alignment file
Hi,
I have one file with one column and several hundred entries

File1:
Code:
NA1
NA2
NA3

And now I need to run a command within a mapping aligner tool to insert these sample names into a sequence alignment file (SAM) such that they look like this

Code:
@RG    ID:Library1 SM:NA1 PL:Illumina  LB:lib_2x250 DS:hg19 
@RG    ID:Library1 SM:NA2 PL:Illumina  LB:lib_2x250 DS:hg19 
@RG    ID:Library1 SM:NA3 PL:Illumina  LB:lib_2x250 DS:hg19

What I am trying is
Code:
file=samples.txt
while IFS= read -r line
do
bwa mem -M -R "@RG\tID:Library1\tSM:$line\tPL:Illumina\tLB:lib_2x250\tDS:hg19" hg19.fasta R1.fastq.gz R2.fastq.gz > alignment.sam
done < "$file"

The output was not was I desired, it had only one sample name and I also think this just overwrites the output file and perform the same alignment several hundred times, is there any fix for this ?

Thank you
# 2  
Old 11-19-2014
Hmmm... Perhaps:

Code:
file=samples.txt
while IFS= read -r line
do
bwa mem -M -R "@RG\tID:Library1\tSM:$line\tPL:Illumina\tLB:lib_2x250\tDS:hg19" hg19.fasta R1.fastq.gz R2.fastq.gz
done < "$file" > alignment.sam

# 3  
Old 11-19-2014
Thank you, but what's happening is that, its not including all the names at once. Its iterating and as a result will perform the same alignment (bwa mem) again and again, in this cases 500 times... one iteration takes about 30-35 hours...so 500 would take days or weeks...
# 4  
Old 11-19-2014
I know nothing about your bwa utility. How would you use it to update multiple things at once?
# 5  
Old 11-19-2014
Well, usually, when we have multiple files, we put everything into a variable and that would work. For my issue above, after going through several forums I understood that I have to make $file (full of IDs) into a variable to which I append each line in the while loop and then put bwa outside of the loop.. but I have just been struggling with the code..
# 6  
Old 11-19-2014
I am mostly confused because I have no idea what bwa does. Is it necessary to this task or not?
# 7  
Old 11-19-2014
no its not necessary to this task... what I need has to be done before bwa starts
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