Hi All,
anusha@cn1:/raid/development/anusha/python_test/shelltest> cat SRAtoBAM_BN_cp1.sh
#bin/bash
#basename /raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203400/SRR203400.sra
find $1
basename $1anusha@cn1:/raid/development/anusha/python_test/shelltest> ./SRAtoBAM_BN_cp1.sh /raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203400
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203400/SRR203400.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203401
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203401/SRR203401.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203402
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203402/SRR203402.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203403
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203403/SRR203403.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203404
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203404/SRR203404.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203405
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203405/SRR203405.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203406
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203406/SRR203406.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203407
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203407/SRR203407.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203408
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203408/SRR203408.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203409
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203409/SRR203409.sra
SRX062364
I am trying to pipe so that i will get sra name find $1 - | basename $1
Thanks in advance,
Anusha.Ch
anusha@cn1:/raid/development/anusha/python_test/shelltest> cat SRAtoBAM_BN_cp1.sh
#bin/bash
#basename /raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203400/SRR203400.sra
find $1
basename $1anusha@cn1:/raid/development/anusha/python_test/shelltest> ./SRAtoBAM_BN_cp1.sh /raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203400
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203400/SRR203400.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203401
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203401/SRR203401.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203402
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203402/SRR203402.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203403
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203403/SRR203403.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203404
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203404/SRR203404.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203405
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203405/SRR203405.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203406
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203406/SRR203406.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203407
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203407/SRR203407.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203408
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203408/SRR203408.sra
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203409
/raid/databases/ROADMAP/DGF/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX062/SRX062364/SRR203409/SRR203409.sra
SRX062364
I am trying to pipe so that i will get sra name find $1 - | basename $1
Thanks in advance,
Anusha.Ch
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