To Give Sequential Input command *******

[AnushaC]

Hi Everyone ,
If I have a directory with a certain extension for exam all bed graph files in a directory how to sequentially take the input . I want give all bedgraph files to command
unionBedGraphs [OPTIONS] -i FILE1 FILE2 FILE3 ... FILEn like that
don't say for loop if i use for loop it is giving files recursively
raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203400.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203401.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203402.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203403.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203404.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203405.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203406.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203407.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203408.sorted.bam
/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sortbam/SRR203409.sorted.bam
anusha@hn:/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_bam> vim bamtbg.copy.sh
anusha@hn:/raid/development/anusha/python_test
I did try to use
name=`ls *bam`
name2=`echo $name | sed 's/ /,/g'`
but it worked with command line not a to shell program
I did try to use
#!/bin/bash
#PBS -l nodes=1pn=2
for file in `ls $1/*.sorted.bam`
do
#name=`ls $1/*.sorted.bam`
IP=`basename $file .sorted.bam`
chs="/raid/references-andI-indexes/hg19/"
name2=`echo $file| sed 's/ /,/g'`
IP1=`basename $name2 .sorted.bam`
echo $file,$name2,$IP,$IP1

#genomeCoverageBed -ibam $file -g $chs -bg > $2/$OP
done

Still giving me output file by file
please appreciate the help

Thanks,
Anusha.ch

[bruce01]

Try:

files=$(ls *bam)

you seem to want comma separated (from your sed commands), but the 'unionBedGraphs' is given as space separated list so above should do that. But the $() convention should work to define your list.

[rhinoceros]

for f in ../*.bam
do
something with $f
done

or if you just want the file name

for f in ../*.bam
do
name=$(basename "$f")
something with $name
done

You can e.g. echo $name >> list