2

I have a dataset of 30 samples and for each sample, I have 2 fastq files named as follow:

bigSample_1.R1.fq
bigSample_1.R2.fq

where R1 and R2 identify the reading direction of my nucleotide sequence (R1=forward, R2=reverse).

I stored all my fastq file in the same directory on my pc (workDir=/media/sf_16S_analysis/Dermatite_fastq_concat/FastQ/fastq_Join); however, I execute my bash shell script using a Virtual machine.

Now I should want to create a manifest-file.csv with the followed structure:

sample-id,absolute-filepath,direction
sample-1,$PWD/some/filepath/sample1_R1.fastq,forward
sample-1,$PWD/some/filepath/sample1_R2.fastq,reverse

More in detail: the manifest file must be a comma-separated (i.e., .csv) text file. The first field on each line is the sample identifier, the second field is the absolute filepath, and the third field is the read direction. The first line in the file is not blank must be the header line:

sample-id,absolute-filepath,direction.

Now my question is: there is a way to read the list of my files .fq in the workDir and create the manifest-file.csv using a script?

  • Sure. The only issue is that you haven't shown where to get the sample ID from. The crowd here are generally not bioinformaticians, and they don't know what a FastQ file looks like. If you could show an example, it would make it easier for others to help you. Also, you seem to be mentioning two systems: A virtual machine and a "PC". Why do you mention this and may this affect the question? – Kusalananda Mar 13 at 16:29
0

Is this anywhere near what you are looking for?

echo "sample-id,absolute-filepath,direction" > manifest
for f in *.fq; do
  dir="forward"
  g=$(echo $f | grep -Po "(?<=\.R)[0-9](?=\.fq)")
  if [ $g -eq 2 ]; then
    dir="reverse"
  fi
  echo ${f%%.*},$PWD/$f,$dir
done >> manifest
cat manifest

Assumes there is only R1 and R2 and that you execute from the containing directory

  • What are the assumptions you made about the sample ID here? Note that the sample ID in the question does not seem to be taken from the filename. Why are all variables unquoted and are you assuming that no value will contain a comma? – Kusalananda Mar 13 at 16:34
  • @Kulasananda I could only assume that the intent was that the original filenames are composed sampleref.R[12].fq. The OP post is inconsistent in naming. – bu5hman Mar 13 at 16:38
  • @Kulasananda $g is a single integer doesn't need quoting, OP space discipline is underscores, ditto re $f quoting and if OP puts commas in a sample ID / filename then ..... he has broken the CSV paradigm anyway. – bu5hman Mar 13 at 16:49
1

With the same approach as bu5hman, i.e. assuming that the sample ID is the part of the filename up to the first dot:

#!/bin/sh

csv_print_row () {
    # Outputs a CSV-formatted row of an arbitrary number of fields.
    # Will quote fields containing commas. That's all.

    for field do
        case $field in
            *,*) set -- "$@" "\"$field\"" ;;
            *)   set -- "$@" "$field"
        esac
        shift
    done

    # The fields are now (possibly quoted) in the list of positional parameters.
    # Print this list as a comma-delimited string:
    ( IFS=,; printf "%s\n" "$*" )
}

# Output header
csv_print_row "sample_id" "absolute-filepath" "direction"

# Loop over the *.fq files in the current directory
for fastq in *.fq; do
    # The sample ID is the filename up to the first dot.
    sample_id=${fastq%%.*}

    # Figure out the direction of the sample
    case $fastq in
        *.R1.*) dir=forward ;;
        *.R2.*) dir=reverse ;;
        *)      dir=unknown
    esac

    # Output row for this sample
    csv_print_row "$sample_id" "$PWD/$fastq" "$dir"
done

Testing:

$ ls -l
total 4
-rw-r--r--  1 kk  wheel    0 Mar 13 18:01 sample-1.R1.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:01 sample-1.R2.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:01 sample-2.R1.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:01 sample-2.R2.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:01 sample-3.R1.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:01 sample-3.R2.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:01 sample-4.R1.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:01 sample-4.R2.fq
-rw-r--r--  1 kk  wheel  629 Mar 13 18:00 script.sh
-rw-r--r--  1 kk  wheel    0 Mar 13 18:02 strange, sample.R1.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:02 strange, sample.R2.fq
-rw-r--r--  1 kk  wheel    0 Mar 13 18:02 strange, sample.R3.fq
$ sh script.sh
sample_id,absolute-filepath,direction
sample-1,/tmp/shell-yash.zm5cvzG6/sample-1.R1.fq,forward
sample-1,/tmp/shell-yash.zm5cvzG6/sample-1.R2.fq,reverse
sample-2,/tmp/shell-yash.zm5cvzG6/sample-2.R1.fq,forward
sample-2,/tmp/shell-yash.zm5cvzG6/sample-2.R2.fq,reverse
sample-3,/tmp/shell-yash.zm5cvzG6/sample-3.R1.fq,forward
sample-3,/tmp/shell-yash.zm5cvzG6/sample-3.R2.fq,reverse
sample-4,/tmp/shell-yash.zm5cvzG6/sample-4.R1.fq,forward
sample-4,/tmp/shell-yash.zm5cvzG6/sample-4.R2.fq,reverse
"strange, sample","/tmp/shell-yash.zm5cvzG6/strange, sample.R1.fq",forward
"strange, sample","/tmp/shell-yash.zm5cvzG6/strange, sample.R2.fq",reverse
"strange, sample","/tmp/shell-yash.zm5cvzG6/strange, sample.R3.fq",unknown

To create your manifest:

sh script.sh >manifest-file.csv

Note that this would generate invalid CSV output if any filename contains double quotes.

To properly handle the quoted fields that contain double quotes, you would have to use something like

csv_print_row () {
    # Outputs a CSV-formatted row of an arbitrary number of fields.

    # Quote fields that needs quoting
    for field do
        case $field in
            *[,\"]*) set -- "$@" "\"$field\"" ;;
            *)       set -- "$@" "$field"
        esac
        shift
    done

    # Double up internal double quotes in fields that have been quoted
    for field do
        case $field in
            '"'*'"'*'"')
                field=$( printf '%s\n' "$field" | sed 's/"/""/g' )
                # Now remove the extra quote at the start and end
                field=${field%\"}
                field=${field#\"}
        esac
        set -- "$@" "$field"
        shift
    done

    ( IFS=,; printf "%s\n" "$*" )
}

This still does not do the right thing for fields that contain newlines, but to handle that would bring us outside the scope of this question.

See also:

  • Like the globbed case. One for the toolbox. – bu5hman Mar 14 at 10:24

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