I have a large directory of files (100+) that I'd like to pass through a program via the terminal.
The files are paired and all follow a naming scheme like such:
TS-8_S53_L001_R1_001.fastq
TS-8_S53_L001_R2_001.fastq
RS-9_S54_L001_R1_001.fastq
RS-9_S54_L001_R2_001.fastq
And the program execution looks like:
Seqprogram -i1 Blah_R1_001.fastq -i2 Blah_R2_001.fastq -o Blah_paired.fastq
All of these files are in one directory.
I'd like to able to run the program on all of the files, using the files paired together in the proper sequence (R1 files are passed through i1, the R1 and R2 files have the same base name) and the output file (-o) is saved under the base name with some identifier attached ("_paired", etc).
I've envisioned on how I'd do this over Python; however, I am trying to get better with BASH.
I'm familiar with how one might call multiple files into a single command; i.e., uncompressing all .gz files in a particular directory
gunzip "*.gz"
But this command has two inputs, and the inputs must be ordered, so the wildcard scheme isn't sufficient.
Thanks
Use a wildcard to get one file of the pair, and then use parameter substitution to get the other corresponding filenames.
for i1 in *_R1_001.fastq; do
i2=${i1/R1_001/R2_001}
paired=${i1/R1_001/paired}
Seqprogram -i1 "$i1" -i2 "$i2" -o "$paired"
done
The easiest way to do this is to match a single one of the three filenames patterned, and to modify it to get the other two.
That is to say:
for r1file in *_R1_*.fastq; do
r2file=${r1file/_R1_/_R2_}
pairfile=${r1file%_R1_*}_paired.fastq
Seqprogram -i1 "$r1file" -i2 "$r2file" -o "$pairfile"
done
Related
I am using a unix based program. I want to automate the code so as not to copy and paste data one by one. For this, I need to define line-by-line data in a file as a variable for the code
The program converts xyz coordinates to local coordinates. How can I run the coordinates in the xyz_coordinates file I created, one by one, in the code below? In the program I use, the conversion code works like this:
echo 4208830.039709186 2334850.551667509 4171267.377406844 -6.753E-01 4.493E-01 2.849E-01 | xyz2env.py
and this is the file i am trying to run:
2679689.926729193 -727950.9964290063 5722789.538975053 7.873E-02 3.466E-01 6.410E-01
2679689.927123377 -727950.9971557076 5722789.540522 7.912E-02 3.458E-01 6.425E-01
2679689.930567728 -727950.9979971027 5722789.550832021 8.257E-02 3.450E-01 6.528E-01
2679689.931029495 -727950.9992263148 5722789.549927638 8.303E-02 3.438E-01 6.519E-01
2679689.929031829 -727950.9981009626 5722789.546359798 8.103E-02 3.449E-01 6.484E-01
........
and it goes on like this. Also, there are spaces between the lines. Will this be a problem?
You can use xargs to invoke the command for a specific number of arguments (6 in your case) and have the advantage of skipping empty lines automatically
< file.txt xargs -n 6 xyz2env.py
I'm new to bash and would like your help; couldn't find an answer for this case.
I'm trying to check if the files in one directory exist in another directory
Let's say I have the path /home/public/folder/ (here I have several files)
and I want to check if the files exist in /home/private/folder2
I tried that
for file in $firstPath/*
do
if [ -f $file ]; then
(ask if to over write etc.. rest of the code)
And also
for file in $firstPath/*
do
if [ -f $file/$secondPath ]; then
(ask if to over write etc.. rest of the code)
Both don't work; it seems that in the first case, it compares the files in the first path (so it always ask me if I want to overwrite although it doesn't exist in the second path)
And in the second case, it doesn't go inside the if statement.
How could I fix that?
When you have a construct like for file in $firstPath/*, the value of $file is going to include the value of $firstPath, which does not exist within $secondPath. You need to strip the path in order to get the bare filename.
In traditional POSIX shell, the canonical way to do this was with an external tool called basename. You can, however, achieve what is generally thought to be equivalent functionality using Parameter Expansion, thus:
for file in "$firstPath"/*; do
if [[ -f "$secondPath/${file##*/}" ]]; then
# file exists, do something
fi
done
The ${file##*/} bit is the important part here. Per the documentation linked above, this means "the $file variable, with everything up to the last / stripped out." The result should be the same as what basename produces.
As a general rule, you should quote your variables in bash. In addition, consider using [[ instead of [ unless you're actually writing POSIX shell scripts which need to be portable. You'll have a more extensive set of tests available to you, and more predictable handling of variables. There are other differences too.
I am new to Linux and I'm trying to look for an ID number within a .bz2 file. Seems like a fairly straight forward requirement, however I cannot find the correct command anywhere online. I believe I need to use bzgrep.
I want to look for '123456' in the file Bulk9876.bz2
How would I construct this command?
You probably just need to tell grep that it's okay to parse that data as text:
bzgrep -a 123456 Bulk9876.bz2
If you're trying to view the compressed data (rather than decompressing it and searching the decompressed data), just use grep -a ….
Otherwise, it might make sense to verify that the desired string is even present in the file; bunzip2 it and grep -a the decompressed file. If that works, the problem is in your bzgrep instance (which is odd because it should be using the same decompression library as bunzip2).
I have a perl script that traverses a set of directories and when it hits one of them it blows up with an Invalid Argument and I want to be able to programmatically skip it. I thought I could start by finding out the file type with the file command but it too blows up like this:
$ file /sys/devices/virtual/net/br-ex/speed
/sys/devices/virtual/net/br-ex/speed: ERROR: cannot read `/sys/devices/virtual/net/br-ex/speed' (Invalid argument)
If I print out the mode of the file with the perl or python stat function it tells me 33060 but I'm not sure what all the bits mean and I'm hoping a particular one would tell me not to try to look inside. Any suggestions?
To understand the stats number you got, you need to convert the number to octal (in python oct(...)).
Then you'll see that 33060 interprets to 100444. You're interested only in the last three digits (444). The first digit is file owner permissions, the second is group and the third is everyone else.
You can look at each of the numbers (in your case all are 4) as 3 binary bits in this order:
read-write-execute.
Since in your case owner, group & other has 4, it is translated (for all of them) to 100 (in binary) which means that only the read bit is on for all three - meaning that all three can only read the file.
As far as file permissions go, you should have been successful reading /sys/devices/virtual/net/br-ex/speed.
There are two reasons for the read to fail:
- Either speed is a directory, (directories require execute permissions to read inside).
- Or it's a special file - which can be tested using the -f flag in perl or bash, or using os.path.isfile(...) in python.
Anyhow, you can use the following links to filter files & directories according to their permissions in the 3 languages you mentioned:
ways to test permissions in perl.
ways to test permissions in python.
ways to test permissions in bash.
Not related to this particular case, but I hit the same error when I ran it on a malicious ELF (Linux executable) file. In that case it was because the program headers of the ELF was intentionally corrupted. Looking at the source code for file command, this is clear as it checks the ELF headers and bails out with the same error in case the headers are corrupted:
/*
* Loop through all the program headers.
*/
for ( ; num; num--) {
if (pread(fd, xph_addr, xph_sizeof, off) <
CAST(ssize_t, xph_sizeof)) {
file_badread(ms);
return -1;
}
TLDR; The file command checks not only the magic bytes, but it also performs other checks to validate a file type.
I have ~ 60K bibliographic records, which can be identified by system number. These records also hold full-text (individudal text files named by system number).
I have lists of system numbers in bunches of 5K and I need to find a way to copy only the text files from each 5K list.
All text files are stored in a directory (/fulltext) and are named something along these lines:
014776324.txt.
The 5k lists are plain text stored in separated directories (e.g. /5k_list_1, 5k_list_2, ...), where each system number matches to a .txt file.
For example: bibliographic record 014776324 matches to 014776324.txt.
I am struggling to find a way to copy into the 5k_list_* folders only the corresponding text files.
Any idea?
Thanks indeed,
Let's assume we invoke the following script this way:
./the-script.sh fulltext 5k_list_1 5k_list_2 [...]
Or more succinctly:
./the-script.sh fulltext 5k_list_*
Then try using this (totally untested) script:
#!/usr/bin/env bash
set -eu # enable error checking
src_dir=$1 # first argument is where to copy files from
shift 1
for list_dir; do # implicitly consumes remaining args
while read bibliographic record sys_num rest; do
cp "$src_dir/$sys_num.txt" "$list_dir/"
done < "$list_dir/list.txt"
done