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Check NCBI if you already uploaded a read set

I have a large number of fastq files locally and most of them have been uploaded to sra. Some might not have been. Can I check against SRA if any particular fastq file has been uploaded already? I feel like it might involve downloading a large spreadsheet of every sra entry for a given pathogen, checking the number of spots against the number of reads I have, and then if it matches, verify with a hashsum.

Get the list of possible accessions from NCBI

# Get all metadata from the Listeria NCBI Pathogens
cat ~/GWA/projects/SneakerNet/ncbiPathogens/data/ftp.ncbi.nlm.nih.gov/pathogen/Results/Listeria/latest_snps/Metadata/PDG000000001.3974.metadata.tsv | sort | gzip -c9 > PDG000000001.3974.metadata.tsv.gz
# extract any SRA run ID
zcat PDG000000001.3974.metadata.tsv | perl -lane 'while(/([DES]RR\d+)/g){print $1;}' > SRA_run.txt
zcat PDG000000001.3974.metadata.tsv | perl -lane 'while(/([DES]RS\d+)/g){print $1;}' > SRS_run.txt
# Get the number of spots per SRA ID
nohup efetch -input SRA_run.txt -db SRA > Listeria.SRR.csv 2> Listeria.SRR.csv.log &
nohup efetch -input SRS_run.txt -db SRA > Listeria.SRS.csv 2> Listeria.SRS.csv.log &

# Make a two column file with SRR identifier and number of spots
# Create gz file to help with disk I/O times when searching later
cut -f4,25 -d, Listeria.SRS.csv Listeria.SRR.csv | sort -nr | gzip -9c > spots.csv.gz

Check my number of spots vs NCBI

zcat testdata/PNUSAL001024_[12].fastq.gz | fasten_metrics | sed 's/^/#/' | column -t
#totalLength  numReads  avgReadLength  avgQual
#305569340    2094942   145.86052      37.695873

# Take the number of reads and divide by 2 to get spots
zgrep $((2094942/2)) spots.csv.gz | sed 's/^/#/'
#1047471,SRS716008

Automate it

# Loop through all R1 files
dir=testdata
for R1 in $dir/*_R1_*.fastq.gz $dir/*_1.fastq.gz; do
    R2=${R1/_1.fastq.gz/_2.fastq.gz}
    R2=${R2/_R1_/_R2_}

    echo "Looking at $R1 and $R2 ..."

    # get the number of spots in the local fastq 
    numReads=$(zcat $R1 $R2 | fasten_metrics | tail -n 1 | cut -f 2)
    SRS=$(zgrep $(($numReads/2)) spots.csv.gz | cut -f2 -d, | sort -n | uniq)

    # Even though only one SRS is expected, more could be found and so loop through them
    # If the SRS is found, then mark for later verification
    (
        for srs_acc in $SRS; do
            echo -e "$srs_acc\t$R1\t$R2"
        done
    ) | gzip -9c >> spots_found_on_ncbi.txt.gz
    # If the SRS is not found, then it is at least not found in NCBI Pathogens and so
    # mark it for safe keeping
    (
        if [ ! "$SRS" ]; then
            echo $R1 $R2
        fi
    ) >> not_on_ncbi.txt
done

# Some results seem to be duplicated a ton and so let's mostly ignore them
zcat spots_found_on_ncbi.txt.gz | perl -lane '
  next if($F[1]++ > 10); 
  print;
' > spots_found_on_ncbi.txt && \
  gzip -fv9 spots_found_on_ncbi.txt

# TODO download fastq from NCBI and compare against local fastq file
# To recap: not_on_ncbi.txt represents reads not already on NCBI for sure, but
# spots_found_on_ncbi.txt represents reads that _might_ be on NCBI.
# We need to verify the reads from spots_found_on_ncbi.txt and either:
#   * (not verified) add these reads to not_on_ncbi.txt 
#   * or, (verified) add these reads to a new file found_on_ncbi.txt
mashThreshold=0.95
k=32
stackSize=10000
parentTempdir="fasterq-dump"
zcat spots_found_on_ncbi.txt.gz | shuf | xargs -P 4 -L 1 bash -c '
  SRS=$0
  localR1=$1
  localR2=$2
  if [[ $(stat -c%s "$localR1") -lt 1000 || $(stat -c%s "$localR2") -lt 1000 ]]; then
    echo "Error: One or both files are smaller than 1000 bytes." >&2
    ls -lhL $localR1 $localR2 >&2
    exit 1
  fi

  perl scripts/checkLocalVsNcbiWithMash.pl --R1 $localR1 --R2 $localR2 --SRS $SRS
' > checkNcbiWithMash.tsv

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