find-best-timeseries.sh

#!/usr/bin/env bash

if [ ! -e rothman.unenriched.lengths.simple ]; then
    cat rothman.unenriched.simple | \
        while read accession date wtp ; do
            echo $accession $date $wtp \
                 $(
                aws s3 cp s3://prjna729801/${accession}_1.fastq.gz - \
                    2>/dev/null | \
                    gunzip | \
                    head -n 2 | \
                    tail -n 1 | \
                    wc -c)
        done | tr ' ' '\t' > rothman.unenriched.lengths.simple
fi

if [ ! -e longest-timeseries.tsv ] ; then
    cat rothman.unenriched.lengths.simple | \
        ./find-best-timeseries.py > longest-timeseries.tsv
fi

if [ ! -e longest-timeseries-with-lengths.tsv ]; then
  cat longest-timeseries.tsv | \
      awk '{print $1}' | \
      xargs -P 32 -I {} bash -c \
          "aws s3 cp s3://prjna729801/{}_1.fastq.gz - | \
           gunzip | \
           grep -c ^@ > {}.n_reads"

  cat longest-timeseries.tsv | \
      while read accession date wtp ; do
          echo $accession $date $wtp $(cat $accession.n_reads)
      done | tr ' ' '\t' > longest-timeseries-with-lengths.tsv
fi