comparison merge_pcr_duplicates.py @ 58:bbbae1ee87e0 draft default tip

fix for flexbar with small data issue

57:537657678b2b

    # prepare alinments
    syscall2 = "cat " + args.alignments + " | awk -F \"\\t\" 'BEGIN{OFS=\"\\t\"}{split($4, a, \" \"); $4 = a[1]; print}'| sort --compress-program=gzip -k4,4 > " + tmpdir + "/alns.csv"
    check_call(syscall2, shell=True)

    # join barcode library and alignments
    syscall3 = "cat " + args.bclib + " | awk 'BEGIN{OFS=\"\\t\"}NR%4==1{gsub(/^@/,\"\"); id=$1}NR%4==2{bc=$1}NR%4==3{print id,bc}' | sort --compress-program=gzip -k1,1 | join -1 1 -2 4 - " + tmpdir + "/alns.csv " + " | awk 'BEGIN{OFS=\"\\t\"}$4!~/N/{print $3,$4,$5,$2,$6,$7}' | datamash --sort -g 1,2,3,4,6 count 4 | awk 'BEGIN{OFS=\"\\t\"}$4!~/N/{print $1,$2,$3,$4,$6,$5}' > " + args.outfile
    # 'chrom', 'start', 'stop', 'bc', 'ndupes', 'strand'
    check_call(syscall3, shell=True)
finally:
    logging.debug("removed tmpdir: " + tmpdir)
    rmtree(tmpdir)

58:bbbae1ee87e0

    # prepare alinments
    syscall2 = "cat " + args.alignments + " | awk -F \"\\t\" 'BEGIN{OFS=\"\\t\"}{split($4, a, \" \"); $4 = a[1]; print}'| sort --compress-program=gzip -k4,4 > " + tmpdir + "/alns.csv"
    check_call(syscall2, shell=True)

    # join barcode library and alignments
    # after join: id, bc, chr, start, stop, mapscore, strand
    # after datamash: bc, chr, start, stop, strand, ndupes, idrepresentative
    syscall3 = "cat " + \
        args.bclib + \
        " | awk 'BEGIN{OFS=\"\\t\"}NR%4==1{gsub(/^@/,\"\"); id=$1}NR%4==2{bc=$1}NR%4==3{print id,bc}' " + \
        " | sort --compress-program=gzip -k1,1 | join -1 1 -2 4 - " + tmpdir + "/alns.csv " + \
        " | awk 'BEGIN{OFS=\"\\t\"}$2!~/N/{print $1,$2,$3,$4,$5,$6,$7}' " + \
        " | datamash --sort -g 2,3,4,5,7 count 2 first 1 " + \
        " | awk 'BEGIN{OFS=\"\\t\"}{print $2,$3,$4,$7,$6,$5}' > " + args.outfile
    check_call(syscall3, shell=True)
finally:
    logging.debug("removed tmpdir: " + tmpdir)
    rmtree(tmpdir)