Mercurial > repos > mbernt > fasta_regex_finder
annotate fastaregexfinder.py @ 0:269c627ae9f4 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
author | mbernt |
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date | Wed, 20 Jun 2018 11:06:57 -0400 |
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children | 9a811adb714f |
rev | line source |
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0
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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1 #!/usr/bin/env python |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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2 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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3 import re |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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4 import sys |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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5 import string |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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6 import argparse |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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7 import operator |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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8 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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9 VERSION='0.1.1' |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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10 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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11 parser = argparse.ArgumentParser(description=""" |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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12 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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13 DESCRIPTION |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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14 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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15 Search a fasta file for matches to a regex and return a bed file with the |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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16 coordinates of the match and the matched sequence itself. |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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17 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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18 Output bed file has columns: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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19 1. Name of fasta sequence (e.g. chromosome) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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20 2. Start of the match |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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21 3. End of the match |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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22 4. ID of the match |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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23 5. Length of the match |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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24 6. Strand |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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25 7. Matched sequence as it appears on the forward strand |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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26 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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27 For matches on the reverse strand it is reported the start and end position on the |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
parents:
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28 forward strand and the matched string on the forward strand (so the G4 'GGGAGGGT' |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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29 present on the reverse strand is reported as ACCCTCCC). |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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30 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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31 Note: Fasta sequences (chroms) are read in memory one at a time along with the |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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32 matches for that chromosome. |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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33 The order of the output is: chroms as they are found in the inut fasta, matches |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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34 sorted within chroms by positions. |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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35 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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36 EXAMPLE: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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37 ## Test data: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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38 echo '>mychr' > /tmp/mychr.fa |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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39 echo 'ACTGnACTGnACTGnTGAC' >> /tmp/mychr.fa |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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40 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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41 fastaRegexFinder.py -f /tmp/mychr.fa -r 'ACTG' |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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42 mychr 0 4 mychr_0_4_for 4 + ACTG |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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43 mychr 5 9 mychr_5_9_for 4 + ACTG |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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44 mychr 10 14 mychr_10_14_for 4 + ACTG |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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45 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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46 fastaRegexFinder.py -f /tmp/mychr.fa -r 'ACTG' --maxstr 3 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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47 mychr 0 4 mychr_0_4_for 4 + ACT[3,4] |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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48 mychr 5 9 mychr_5_9_for 4 + ACT[3,4] |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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49 mychr 10 14 mychr_10_14_for 4 + ACT[3,4] |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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50 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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51 less /tmp/mychr.fa | fastaRegexFinder.py -f - -r 'A\w\wGn' |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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52 mychr 0 5 mychr_0_5_for 5 + ACTGn |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
mbernt
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53 mychr 5 10 mychr_5_10_for 5 + ACTGn |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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54 mychr 10 15 mychr_10_15_for 5 + ACTGn |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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55 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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56 DOWNLOAD |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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57 fastaRegexFinder.py is hosted at https://github.com/dariober/bioinformatics-cafe/tree/master/fastaRegexFinder |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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58 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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59 """, formatter_class= argparse.RawTextHelpFormatter) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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60 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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61 parser.add_argument('--fasta', '-f', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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62 type= str, |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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63 help='''Input fasta file to search. Use '-' to read the file from stdin. |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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64 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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65 ''', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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66 required= True) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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67 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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68 parser.add_argument('--regex', '-r', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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69 type= str, |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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70 help='''Regex to be searched in the fasta input. |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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71 Matches to the reverse complement will have - strand. |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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72 The default regex is '([gG]{3,}\w{1,7}){3,}[gG]{3,}' which searches |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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73 for G-quadruplexes. |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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74 ''', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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75 default= '([gG]{3,}\w{1,7}){3,}[gG]{3,}') |
269c627ae9f4
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76 |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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77 parser.add_argument('--matchcase', '-m', |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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78 action= 'store_true', |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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79 help='''Match case while searching for matches. Default is |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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80 to ignore case (I.e. 'ACTG' will match 'actg'). |
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81 ''') |
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82 |
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83 parser.add_argument('--noreverse', |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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84 action= 'store_true', |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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85 help='''Do not search the reverse complement of the input fasta. |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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86 Use this flag to search protein sequences. |
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87 ''') |
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88 |
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89 parser.add_argument('--maxstr', |
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90 type= int, |
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91 required= False, |
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92 default= 10000, |
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93 help='''Maximum length of the match to report in the 7th column of the output. |
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94 Default is to report up to 10000nt. |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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95 Truncated matches are reported as <ACTG...ACTG>[<maxstr>,<tot length>] |
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96 ''') |
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97 |
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98 parser.add_argument('--seqnames', '-s', |
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99 type= str, |
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100 nargs= '+', |
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101 default= [None], |
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102 required= False, |
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103 help='''List of fasta sequences in --fasta to |
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104 search. E.g. use --seqnames chr1 chr2 chrM to search only these crhomosomes. |
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105 Default is to search all the sequences in input. |
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106 ''') |
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107 parser.add_argument('--quiet', '-q', |
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108 action= 'store_true', |
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109 help='''Do not print progress report (i.e. sequence names as they are scanned). |
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110 ''') |
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111 |
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112 |
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113 |
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114 parser.add_argument('--version', '-v', action='version', version='%(prog)s ' + VERSION) |
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115 |
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116 |
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117 args = parser.parse_args() |
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118 |
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119 " --------------------------[ Check and parse arguments ]---------------------- " |
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120 |
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121 if args.matchcase: |
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122 flag= 0 |
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123 else: |
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124 flag= re.IGNORECASE |
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125 |
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126 " ------------------------------[ Functions ]--------------------------------- " |
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127 |
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128 def sort_table(table, cols): |
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129 """ Code to sort list of lists |
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130 see http://www.saltycrane.com/blog/2007/12/how-to-sort-table-by-columns-in-python/ |
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131 |
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132 sort a table by multiple columns |
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133 table: a list of lists (or tuple of tuples) where each inner list |
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134 represents a row |
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135 cols: a list (or tuple) specifying the column numbers to sort by |
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136 e.g. (1,0) would sort by column 1, then by column 0 |
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137 """ |
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138 for col in reversed(cols): |
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139 table = sorted(table, key=operator.itemgetter(col)) |
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140 return(table) |
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141 |
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142 def trimMatch(x, n): |
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143 """ Trim the string x to be at most length n. Trimmed matches will be reported |
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144 with the syntax ACTG[a,b] where Ns are the beginning of x, a is the length of |
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145 the trimmed strng (e.g 4 here) and b is the full length of the match |
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146 EXAMPLE: |
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147 trimMatch('ACTGNNNN', 4) |
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148 >>>'ACTG[4,8]' |
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149 trimMatch('ACTGNNNN', 8) |
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150 >>>'ACTGNNNN' |
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151 """ |
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152 if len(x) > n and n is not None: |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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153 m= x[0:n] + '[' + str(n) + ',' + str(len(x)) + ']' |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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154 else: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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155 m= x |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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156 return(m) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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157 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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158 def revcomp(x): |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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159 """Reverse complement string x. Ambiguity codes are handled and case conserved. |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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160 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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161 Test |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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162 x= 'ACGTRYSWKMBDHVNacgtryswkmbdhvn' |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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163 revcomp(x) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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164 """ |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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165 compdict= {'A':'T', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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166 'C':'G', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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167 'G':'C', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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168 'T':'A', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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169 'R':'Y', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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170 'Y':'R', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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171 'S':'W', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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172 'W':'S', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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173 'K':'M', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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174 'M':'K', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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175 'B':'V', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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176 'D':'H', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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177 'H':'D', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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178 'V':'B', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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179 'N':'N', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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180 'a':'t', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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181 'c':'g', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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182 'g':'c', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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183 't':'a', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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184 'r':'y', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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185 'y':'r', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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186 's':'w', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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187 'w':'s', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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188 'k':'m', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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189 'm':'k', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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190 'b':'v', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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191 'd':'h', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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192 'h':'d', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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193 'v':'b', |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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194 'n':'n'} |
269c627ae9f4
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195 xrc= [] |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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196 for n in x: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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197 xrc.append(compdict[n]) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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198 xrc= ''.join(xrc)[::-1] |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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199 return(xrc) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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200 # ----------------------------------------------------------------------------- |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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201 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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202 psq_re_f= re.compile(args.regex, flags= flag) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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203 ## psq_re_r= re.compile(regexrev) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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204 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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205 if args.fasta != '-': |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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206 ref_seq_fh= open(args.fasta) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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207 else: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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208 ref_seq_fh= sys.stdin |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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209 |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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210 ref_seq=[] |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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211 line= (ref_seq_fh.readline()).strip() |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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212 chr= re.sub('^>', '', line) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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213 line= (ref_seq_fh.readline()).strip() |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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214 gquad_list= [] |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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215 while True: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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216 if not args.quiet: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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217 sys.stderr.write('Processing %s\n' %(chr)) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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218 while line.startswith('>') is False: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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219 ref_seq.append(line) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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220 line= (ref_seq_fh.readline()).strip() |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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221 if line == '': |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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|
222 break |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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223 ref_seq= ''.join(ref_seq) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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224 if args.seqnames == [None] or chr in args.seqnames: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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225 for m in re.finditer(psq_re_f, ref_seq): |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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226 matchstr= trimMatch(m.group(0), args.maxstr) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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227 quad_id= str(chr) + '_' + str(m.start()) + '_' + str(m.end()) + '_for' |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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228 gquad_list.append([chr, m.start(), m.end(), quad_id, len(m.group(0)), '+', matchstr]) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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229 if args.noreverse is False: |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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230 ref_seq= revcomp(ref_seq) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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231 seqlen= len(ref_seq) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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232 for m in re.finditer(psq_re_f, ref_seq): |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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233 matchstr= trimMatch(revcomp(m.group(0)), args.maxstr) |
269c627ae9f4
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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234 mstart= seqlen - m.end() |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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235 mend= seqlen - m.start() |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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236 quad_id= str(chr) + '_' + str(mstart) + '_' + str(mend) + '_rev' |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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237 gquad_list.append([chr, mstart, mend, quad_id, len(m.group(0)), '-', matchstr]) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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238 gquad_sorted= sort_table(gquad_list, (1,2,3)) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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239 gquad_list= [] |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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240 for xline in gquad_sorted: |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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241 xline= '\t'.join([str(x) for x in xline]) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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242 print(xline) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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243 chr= re.sub('^>', '', line) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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244 ref_seq= [] |
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245 line= (ref_seq_fh.readline()).strip() |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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246 if line == '': |
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247 break |
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248 |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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249 #gquad_sorted= sort_table(gquad_list, (0,1,2,3)) |
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250 # |
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251 #for line in gquad_sorted: |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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252 # line= '\t'.join([str(x) for x in line]) |
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253 # print(line) |
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254 sys.exit() |