fastq.gz files renaming using python

Question

[mukil.biotek]

Hi all, I have fastq.gz files and I need to rename it

The read names in my files are

389817_001_E01_S49_R1_001.fastq.gz
389817_001_E01_S49_R2_001.fastq.gz
389818_001_A01_S1_R1_001.fastq.gz
389818_001_A01_S1_R2_001.fastq.gz

And i want to transform them in the format:

389817_S49_L001_R1_001.fastq.gz
389817_S49_L001_R2_001.fastq.gz
389818_S1_L001_R1_001.fastq.gz
389818_S1_L001_R2_001.fastq.gz

I tried using python but not working..see below for codes

import os
for i in os.listdir():
    file_name, file_ext = os.path.splitext(i)
    print(os.path.splitext(i))
    file_name, file_ext = os.path.splitext(i)
    print(file_name)    
    file_name1, file_ext1 = os.path.splitext(file_name)
    file_name1
    file_ext1
    print(file_name1.split('_'))
    f_0, f_1, f_2, f_3, f_4, f_5 = file_name1.split('_')
    new_name = print(os.path.join(f_0+'_'+f_3+'_'+'L001'+'_'+f_4+'_'+f_5+file_ext1+file_ext))
    path = '/Users/mukilkavi/Desktop/NAMING'
    os.rename('/Users/mukilkavi/Desktop/NAMING/', new_name)

Any advice will be appreciated...Thanks in advance

[swbarnes2]

I don't know python, but shouldn't that last line concatenate the path and the 'i' file name, and that's the input into os.rename?

[Mensur Dlakic]

How many of these files need renaming? If it is only what you listed, a simple mv command may be good enough.

mv 389817_001_E01_S49_R1_001.fastq.gz 389817_S49_L001_R1_001.fastq.gz

Answer 1

[Pierre Lindenbaum]

how about 'just' using bash.

 ls *.fastq.gz | awk -F '_' '{printf("mv \"%s\" \"%s_%s_L001_%s_%s\"\n",$0,$1,$4,$5,$6);}' > script.bash

check script.bash and then

bash script.bash

Answer 2

[Ram]

for f in *.fastq.gz
    newname=$(echo -n $f | awk -F "_" -vOFS="_" '{print $1,$4,"L001",$5,$6}')
    echo "mv $f $newname"
done

Untested, but should work. Once you test it and everything looks OK, change the echo statement to just mv $f $newname and the files should be renamed.