to aligning all reads with SHRiMP (as automatic)

ahabnar · 11-04-2009, 10:43 AM

Hi,

I'm new in SHRiMP. I have 10 library and for each library, i had used the splitreads.py of SHRiMP to 1000 files. Then, i have 1000 files csfasta type for on library. I had test some of them with rmapper-cs... to align and it's working but i need to run the same command as automatically for the 1000 files csfasta first and for all 10 library.
The command line is like:
./rmapper-cs -m 8 -i -30 -g -35 -e -7 -x -25 -h 70% -v 65% -M 35bp,fast -o 100 -U /root/Desktop/SHRiMP_1_3_0/readsT/1000_to_1999.csfasta /root/Desktop/DB.fasta > /root/Desktop/SHRiMP_1_3_0/results/res_1000_to_1999.out

I try with command find like this one:

#!/bin/bash
#

find /root/Desktop/SHRiMP_1_3_0/readsT/ -name "*.csfasta*" -exec /root/Desktop/SHRiMP_1_3_0/bin/rmapper-cs -m 8 -i -30 -g -35 -e -7 -x -25 -h 70% -v 65% -M 35bp,fast -o 100 -U "{}" /root/Desktop/docShrimp191009/DB.fasta >> /root/Desktop/SHRiMP_1_3_0/results/"{}"res_U_lib1.out {} \;

but it said bad file and nothing in result file

Do you know what's the problem

ps: {} is just to have the name of the file in result, it does't working but for the input file it's ok

ravelna

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11-04-2009, 10:43 AM	#1
ahabnar Junior Member Location: Montreal Join Date: Oct 2009 Posts: 1	to aligning all reads with SHRiMP (as automatic) Hi, I'm new in SHRiMP. I have 10 library and for each library, i had used the splitreads.py of SHRiMP to 1000 files. Then, i have 1000 files csfasta type for on library. I had test some of them with rmapper-cs... to align and it's working but i need to run the same command as automatically for the 1000 files csfasta first and for all 10 library. The command line is like: ./rmapper-cs -m 8 -i -30 -g -35 -e -7 -x -25 -h 70% -v 65% -M 35bp,fast -o 100 -U /root/Desktop/SHRiMP_1_3_0/readsT/1000_to_1999.csfasta /root/Desktop/DB.fasta > /root/Desktop/SHRiMP_1_3_0/results/res_1000_to_1999.out I try with command find like this one: #!/bin/bash # find /root/Desktop/SHRiMP_1_3_0/readsT/ -name ".csfasta" -exec /root/Desktop/SHRiMP_1_3_0/bin/rmapper-cs -m 8 -i -30 -g -35 -e -7 -x -25 -h 70% -v 65% -M 35bp,fast -o 100 -U "{}" /root/Desktop/docShrimp191009/DB.fasta >> /root/Desktop/SHRiMP_1_3_0/results/"{}"res_U_lib1.out {} \; but it said bad file and nothing in result file Do you know what's the problem ps: {} is just to have the name of the file in result, it does't working but for the input file it's ok ravelna