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annotate make-barcodes.awk @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 # The awk code that transforms the one-line fastq record pair into the output that can be sorted
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2 # by barcode.
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3 # Input columns (the 4 FASTQ lines for both reads in a read pair):
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4 # 1: read1 name
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5 # 2: read2 name
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6 # 3: read1 sequence
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7 # 4: read2 sequence
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8 # 5: read1 + line
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9 # 6: read2 + line
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10 # 7: read1 quality
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11 # 8: read2 quality
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12 # Output columns:
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13 # 1: the barcode, put into a canonical form
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14 # 2: the order of the barcode halves ("ab" or "ba")
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15 # 3: read1 name
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16 # 4: sequence of read 1, minus the 12bp barcode and 5bp invariant sequence
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17 # 5: read1 quality scores, minus the same first 17bp
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18 # 6: read2 name
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19 # 7: sequence of read 2, minus the first 17bp
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20 # 8: read2 quality scores, minus the first 17bp
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21 # The canonical form of the barcode is composed of two concatenated tags, one from each read.
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22 # By default, each tag is the first 12bp of the read. The tag from the first read is the "alpha" and
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23 # the tag from the second is the "beta". The barcode is formed by concatenating them in an order
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24 # determined by a string comparison of the two. The lesser tag is first (if they are equal, the
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25 # beta is first, but then you have bigger problems).
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26
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27 BEGIN {
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28 FS = "\t"
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29 OFS = "\t"
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30 # The number of bases from the start of each read that form the two halves of the barcode.
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31 # (this should be half the size of the full, canonical barcode).
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32 if (TAG_LEN == "") {
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33 TAG_LEN = 12
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34 }
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35 # The number of bases in the read that are between the barcode and the start of the actual sample
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36 # sequence (the restriction site in the Loeb 2014 protocol).
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37 if (INVARIANT == "") {
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38 INVARIANT = 5
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39 }
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40 }
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41
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42 $3 && $4 {
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43 alpha = substr($3, 1, TAG_LEN)
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44 beta = substr($4, 1, TAG_LEN)
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45 if (alpha < beta) {
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46 barcode = alpha beta
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47 order = "ab"
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48 } else {
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49 barcode = beta alpha
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50 order = "ba"
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51 }
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52 name1 = substr($1, 2)
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53 name2 = substr($2, 2)
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54 seq1 = substr($3, TAG_LEN + INVARIANT + 1)
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55 seq2 = substr($4, TAG_LEN + INVARIANT + 1)
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56 qual1 = substr($7, TAG_LEN + INVARIANT + 1)
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57 qual2 = substr($8, TAG_LEN + INVARIANT + 1)
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58 print barcode, order, name1, seq1, qual1, name2, seq2, qual2
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59 }