Mercurial > repos > iuc > rcorrector
annotate FilterUncorrectabledPEfastq.py @ 0:9a0b65ad3c84 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
author | iuc |
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date | Thu, 13 Sep 2018 07:00:00 -0400 |
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children | 6703b98884a2 |
rev | line source |
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0
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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1 """ |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
|
2 author: adam h freedman |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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3 afreedman405 at gmail.com |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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4 data: Fri Aug 26 10:55:18 EDT 2016 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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5 This script takes as an input Rcorrector error corrected Illumina paired-reads |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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6 in fastq format and: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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7 1. Removes any reads that Rcorrector indentifes as containing an error, |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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8 but can't be corrected, typically low complexity sequences. For these, |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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9 the header contains 'unfixable'. |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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10 2. Strips the ' cor' from headers of reads that Rcorrector fixed, to avoid |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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11 issues created by certain header formats for downstream tools. |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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12 3. Write a log with counts of (a) read pairs that were removed because one end |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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13 was unfixable, (b) corrected left and right reads, (c) total number of |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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14 read pairs containing at least one corrected read. |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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15 Currently, this script only handles paired-end data, and handle either unzipped |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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16 or gzipped files on the fly, so long as the gzipped files end with 'gz'. |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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17 """ |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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18 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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19 # import sys |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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20 import argparse |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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21 import gzip |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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22 from itertools import izip_longest |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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23 # izip |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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24 from os.path import basename |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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25 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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26 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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27 def get_input_streams(r1file, r2file): |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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28 if r1file[-2:] == 'gz': |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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29 r1handle = gzip.open(r1file, 'rb') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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30 r2handle = gzip.open(r2file, 'rb') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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31 else: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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32 r1handle = open(r1file, 'r') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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33 r2handle = open(r2file, 'r') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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34 return r1handle, r2handle |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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35 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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36 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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37 def grouper(iterable, n, fillvalue=None): |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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38 "Collect data into fixed-length chunks or blocks" |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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39 # grouper('ABCDEFG', 3, 'x') --> ABC DEF Gxx |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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40 args = [iter(iterable)] * n |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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41 return izip_longest(fillvalue=fillvalue, * args) |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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42 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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43 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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44 if __name__ == "__main__": |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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45 parser = argparse.ArgumentParser(description="options for filtering and logging rCorrector fastq outputs") |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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46 parser.add_argument('-1', '--left_reads', dest='leftreads', type=str, help='R1 fastq file') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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47 parser.add_argument('-2', '--right_reads', dest='rightreads', type=str, help='R2 fastq file') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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48 parser.add_argument('-o', '--out_prefix', dest='outprefix', type=str, help="prefix for filtered fastq output") |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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49 opts = parser.parse_args() |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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50 r1out = open(opts.outprefix + '_' + basename(opts.leftreads).replace('.gz', ''), 'w') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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51 r2out = open(opts.outprefix + '_' + basename(opts.rightreads).replace('.gz', ''), 'w') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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52 r1_cor_count = 0 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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changeset
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53 r2_cor_count = 0 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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54 pair_cor_count = 0 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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55 unfix_count = 0 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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56 r1_stream, r2_stream = get_input_streams(opts.leftreads, opts.rightreads) |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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57 with r1_stream as f1, r2_stream as f2: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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58 R1 = grouper(f1, 4) |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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59 R2 = grouper(f2, 4) |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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60 counter = 0 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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61 for entry in R1: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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62 counter += 1 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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63 if counter % 100000 == 0: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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64 print "%s reads processed" % counter |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
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65 head1, seq1, placeholder1, qual1 = [i.strip() for i in entry] |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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66 head2, seq2, placeholder2, qual2 = [j.strip() for j in R2.next()] |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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67 if 'unfixable' in head1 or 'unfixable' in head2: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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68 unfix_count += 1 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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69 else: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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70 if 'cor' in head1: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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71 r1_cor_count += 1 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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72 if 'cor' in head2: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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73 r2_cor_count += 1 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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74 if 'cor' in head1 or 'cor' in head2: |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
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75 pair_cor_count += 1 |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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76 head1 = head1.split('l:')[0][:-1] # keeps all before the low kmer count statistic and removes the trailing whitespace character |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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77 head2 = head2.split('l:')[0][:-1] |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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78 # head1 = head1.replace(' cor', '') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
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79 # head2 = head2.replace(' cor', '') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
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80 r1out.write('%s\n' % '\n'.join([head1, seq1, placeholder1, qual1])) |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
|
81 r2out.write('%s\n' % '\n'.join([head2, seq2, placeholder2, qual2])) |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
|
82 unfix_log = open('rmunfixable.log', 'w') |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
|
83 unfix_log.write('total PE reads:%s\nremoved PE reads:%s\nretained PE reads:%s\nR1 corrected:%s\nR2 corrected:%s\npairs corrected:%s\n' % (counter, unfix_count, counter - unfix_count, r1_cor_count, r2_cor_count, pair_cor_count)) |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
|
84 r1out.close() |
9a0b65ad3c84
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
iuc
parents:
diff
changeset
|
85 r2out.close() |