shell create new folder - bash

Question

I have many files' path, but I need to copy all files into other location /sample, and I want to copy files into different folders:
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59329/111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59329/111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_2.fq.gz
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59329/clean_111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz.total.info
I want to copy those files into AS34_59329 folder inside /sample
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59328/111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59328/111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_2.fq.gz
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59328/clean_111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz.total.info
I want to copy those file into AS34_59328 folder inside /sample
I write codes to scp all file into /sample folder, but I don't know how to put each files into different sub-directory, like:
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59328/clean_111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz.total.info
put into AS34_59328
#! /bin/bash
while read myline
do
for i in $myline
do
if [ -f $i]; then
#how to put different files into different sub-directory
scp -r $i xxx#191.168.174.43:/sample
fi
done
done < data.list
new changed part
#! /bin/bash
while read myline
do
for i in $myline
do
if [ -f $i ]
then
relname=$(echo $i | sed 's%\(/[^/][^/]*\)\{5\}/%%')
echo $relname
fi
done
done < /home/jesse/T11073_all_3254.fq.list

Answer 1

It appears you need to strip the leading 5 components of the pathname off the filename. Since you don't have spaces in your names (the way you're using for i in $myline precludes that possibility), you can use:
#! /bin/bash
while read myline
do
for i in $myline
do
if [ -f $i ]
then
relname=$(echo $i | sed 's%\(/[^/][^/]*\)\{5\}/%%')
scp -r $i xxx#191.168.174.43:/sample/$relname
fi
done
done < data.list
The regex is just a way of looking for a sequence of five sets of slash followed by one or more non-slashes plus one more slash and deleting them. Since slashes figure prominently in the search, I used % to mark the sections of the s/// operation instead.
For example, given the input:
/a/b/c/d/e/f/g
the output from the sed is:
f/g
Note that this code does not explicitly create directories on the remote machine; it just specifies where the file is to go. If you need to create them too, you will have to investigate ssh, probably, to run mkdir -p /sample/$(dirname $relname) on the remote machine (where the dirname operation can be run either locally or remotely).
Note that scp has a recursive copy mode (-r) which would simplify things considerably if you knew you needed to copy all the files from the local directory to the remote.