[AnushaC]

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

[AnushaC]

HI aLL,
#find $1
#basename $1
#find $1 -type f -print0 | xargs -0 -n1 basename
find -L $1 -type f -print0 | xargs -n1 basename
I was using like this . i am getting like this
xargs: WARNING: a NUL character occurred in the input. It cannot be passed through in the argument list. Did you mean to use the --null option?
SRR203400.sra
more over how can get all the sra files without hardcoding anything

Thanks in advance,
Anusha.Ch

[rhinoceros]

How about you post your code so that you have commented each line separately (what you think it does) so that we might get some idea of what you're trying to do?

[AnushaC]

Hi All,
Here is my problem -- I wrote two shell scripts one for getting all the sra files in given directory ,one for converting from sam file to bam file . Both are working fine but I am getting confused how to pipe my all sra input second program which converts to bam file

This is my first program
#bin/bash
#finding the given sra files in directories and subdirectories and outputing them
find -L $1 -type f -print0 | xargs --null -n1 basename

give me output like this

anusha@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/
SRR203400.sra
SRR203401.sra
SRR203402.sra
SRR203403.sra
SRR203404.sra
SRR203405.sra
SRR203406.sra
SRR203407.sra
SRR203408.sra
SRR203409.sra
now i want to all my sra file and pipe this program

#!/bin/bash
# Taking an SRA input and hg19 reference into variables
sraip=$1
hg19ref=$2
# generating shell pipeline
# 1) using fastq dump to generate fastq file given sra input
#2) using bowtie to map the fastq file to given reference genome
#3) using samtools view to generate bam file from the given sam file
fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 - | samtools view -bS -o $3 -

which converts from sra to bam format

Thanks very much in advance,
Anusha.Ch

[rhinoceros]

Your first script returns a list of filenames, how could your second script know where these files are? One solution would be to make your first script write the full paths of your files to some file and then in the second script you go through that file line by line. Something like:

while read line
do 
something with a $line
done <yourInputListOfFilePaths.txt

[AnushaC]

Hi got it ,
Thanks

Anusha.Ch