bash script for writing the files name and path, and directions of read

Question

[Bioinfonext]

Hi, I am using below script to write the sample name, followed by path of the file and then for R1 it write forward and for R2 it writes reverse: but some of the file it do not write correctly, could you please suggest what is the problem:

sample-id,absolute-filepath,direction

wrong file written: forward file is correct but reverse is not written correctly:

Leaf-T1-FD-R10_S73_L001,/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R10_S73_L001_R1_001.fastq.gz,forward    

Leaf-T1-FD-R20_S73_L001_R1_001.fastq.gz,/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R20_S73_L001_R1_001.fastq.gz,reverse

correct files written:

Leaf-T1-FD-R2_S29_L001,/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R2_S29_L001_R1_001.fastq.gz,forward

Leaf-T1-FD-R2_S29_L001,/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R2_S29_L001_R2_001.fastq.gz,reverse

Script:

#!/bin/bash
# header
echo "sample-id,absolute-filepath,direction"

# PATH to directory holding files, no trailing slash!
TARGET="/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq"
for fileR1 in $TARGET/*_R1_*gz; do
    # $file is the absolute path
    fileR2=$(echo $fileR1 | sed 's/R1/R2/')
    R1=$(basename $fileR1)
    R2=$(basename $fileR2)
    sampleR1=$(echo $R1 | sed 's/_R1_001.fastq.gz//')
    sampleR2=$(echo $R2 | sed 's/_R2_001.fastq.gz//')
    # print the results to stdout
    echo "$sampleR1,$fileR1,forward"
    echo "$sampleR2,$fileR2,reverse"
done

Answer 1

[AK]

Hi Bioinfonext,

Can you check by printing out fileR2 after you did fileR2=$(echo $fileR1 | sed 's/R1/R2/')?

Also, you can add _R1_001.fastq.gz when you use basename. Test with:

$ ls /users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R2_S29_L001_R*
/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R2_S29_L001_R1_001.fastq.gz
/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R2_S29_L001_R2_001.fastq.gz

The following script:

#!/bin/bash
# header
echo "sample-id,absolute-filepath,direction"

# PATH to directory holding files, no trailing slash!
TARGET="/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq"

for fileR1 in $TARGET/*_R1_*gz; do
  # $file is the absolute path
  fileR2=$(echo $fileR1 | sed 's/R1/R2/')
  sampleR1=$(basename $fileR1 _R1_001.fastq.gz)
  sampleR2=$(basename $fileR2 _R2_001.fastq.gz)
  # print the results to stdout
  echo "$sampleR1,$fileR1,forward"
  echo "$sampleR2,$fileR2,reverse"
done

Will return:

sample-id,absolute-filepath,direction
Leaf-T1-FD-R2_S29_L001,/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R2_S29_L001_R1_001.fastq.gz,forward
Leaf-T1-FD-R2_S29_L001,/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R2_S29_L001_R2_001.fastq.gz,reverse

[Bioinfonext]

Hi, other files are written correctly but the problem is with FILES which are having R10 in there name:

like this is not written correctly:

Leaf-T1-FD-R10_S73_L001_R1_001.fastq.gz

Leaf-T1-FD-R10_S73_L001_R2_001.fastq.gz

output by script:

Leaf-T1-FD-R10_S73_L001,/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R10_S73_L001_R1_001.fastq.gz,forward

Leaf-T1-FD-R20_S73_L001_R1_001.fastq.gz,/users/3052771/sharedscratch/Amplicon_data_july_2019/PN0086C_16S-137179427/Amplicon_2019_RNAseq/Leaf-T1-FD-R20_S73_L001_R1_001.fastq.gz,reverse

[AK]

You can change from fileR2=$(echo $fileR1 | sed 's/R1/R2/') to fileR2=$(echo $fileR1 | sed 's/R1_/R2_/').

[Bioinfonext]

Now script is working perfectly after the correction suggested by SMK.

Thanks a lot for your valuable time.

Regards Bioinfonext