Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles
annotate data_manager/install_primer_scheme_bedfiles.py @ 3:a2953ef09fe1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
author | iuc |
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date | Mon, 12 Oct 2020 13:47:03 +0000 |
parents | b3710e492ee4 |
children | 157a5c9ea72a |
rev | line source |
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0
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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1 #!/usr/bin/env python |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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2 |
2
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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3 from __future__ import division, print_function |
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ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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4 |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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5 import argparse |
2
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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6 try: |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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7 from io import StringIO |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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8 except ImportError: |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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9 from StringIO import StringIO |
0
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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10 import json |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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11 import os |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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12 import os.path |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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13 import re |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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14 import sys |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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15 |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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16 import requests |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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17 |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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18 DATA_TABLE_NAME = "primer_scheme_bedfiles" |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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19 |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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20 |
3
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
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21 def write_artic_style_bed(input_file, bed_output_filename): |
2
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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22 with open(bed_output_filename, "w") as bed_output_file: |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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23 for line in input_file: |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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24 fields = line.split("\t") |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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25 if len(fields) < 6: |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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26 # too short to encode the strand format |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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27 exit("invalid format in BED file: {}".format(line.rstrip())) |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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28 try: |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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29 # try and parse field 5 as a number |
3
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
iuc
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30 score = float(fields[4]) |
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b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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31 except ValueError: |
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a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
iuc
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32 # Alright, this is an ARTIC-style bed, |
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
iuc
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33 # which is actually against the specs, but required by the |
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
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34 # ARTIC pipeline. |
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
iuc
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35 pass |
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
iuc
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36 else: |
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
iuc
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37 # This is a regular bed with numbers in the score column. |
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
iuc
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38 # We need to "fix" it for the ARTIC pipeline. |
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
iuc
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39 fields[4] = '_{0}'.format(score) |
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b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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40 bed_output_file.write("\t".join(fields)) |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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41 |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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42 |
0
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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43 def fetch_artic_primers(output_directory, primers): |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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44 primer_sets = { |
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cce5d9327cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
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45 "SARS-CoV-2-ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed", |
cce5d9327cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
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46 "SARS-CoV-2-ARTICv2": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed", |
cce5d9327cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
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47 "SARS-CoV-2-ARTICv3": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed", |
0
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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48 } |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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49 |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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50 data = [] |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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51 for name, url in primer_sets.items(): |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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52 if name not in primers: |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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53 continue |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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54 response = requests.get(url) |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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55 if response.status_code != 200: |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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56 print( |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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57 "Error: download of", |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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58 url, |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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59 "failed with code", |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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60 response.status_code, |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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61 file=sys.stderr, |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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62 ) |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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63 exit(response.status_code) |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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64 bed_output_filename = os.path.join(output_directory, name + ".bed") |
3
a2953ef09fe1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 1e0936cb95a0318809b3306fad43ce444d7682b0"
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65 write_artic_style_bed(StringIO(response.text), bed_output_filename) |
0
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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66 description = name[:-2] + " " + name[-2:] + " primer set" |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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67 data.append(dict(value=name, path=bed_output_filename, description=description)) |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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68 return data |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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69 |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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70 |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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71 def install_primer_file( |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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72 output_directory, input_filename, primer_name, primer_description |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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73 ): |
ae730ecdc7e7
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74 name = re.sub(r"\W", "", str(primer_name).replace(" ", "_")) |
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75 output_filename = os.path.join(output_directory, name + ".bed") |
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76 with open(input_filename) as input_file: |
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77 write_artic_style_bed(input_file, output_filename) |
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78 data = [dict(value=name, description=primer_description, path=output_filename)] |
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79 return data |
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80 |
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81 |
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82 class SplitArgs(argparse.Action): |
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83 def __call__(self, parser, namespace, values, option_string=None): |
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84 setattr(namespace, self.dest, values.split(",")) |
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85 |
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86 |
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87 if __name__ == "__main__": |
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88 parser = argparse.ArgumentParser( |
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89 description="Fetch ARTIC SARS-CoV-2 primer files for Galaxy/IRIDA use" |
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90 ) |
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91 parser.add_argument( |
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92 "--output_directory", default="tmp", help="Directory to write output to" |
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93 ) |
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94 primer_file = parser.add_argument_group() |
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95 primer_file.add_argument( |
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96 "--primer_file", help="BED format file containing primer scheme" |
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97 ) |
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98 primer_file.add_argument( |
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99 "--primer_name", |
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100 help="Name of primer scheme (one word). Required if --primer_file is used", |
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101 ) |
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102 primer_file.add_argument( |
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103 "--primer_description", |
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104 help="Description of primer scheme. Required if --primer_file is used", |
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105 ) |
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106 artic = parser.add_argument_group() |
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107 artic.add_argument( |
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108 "--artic_primers", |
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109 action=SplitArgs, |
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110 help="Comma separated list of primers to fetch", |
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111 ) |
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112 parser.add_argument( |
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113 "galaxy_datamanager_filename", |
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114 help="Galaxy JSON format file describing data manager inputs", |
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115 ) |
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116 args = parser.parse_args() |
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117 |
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118 if args.artic_primers is None and args.primer_file is None: |
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119 print( |
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120 "One of --artic_primers or --primer_file + --primer_name + --primer_description is required.", |
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121 file=sys.stderr, |
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122 ) |
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123 exit(1) |
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124 elif args.primer_file is not None and ( |
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125 args.primer_name is None or args.primer_description is None |
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126 ): |
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127 print( |
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128 "If --primer_file is used --primer_name and --primer_description is also required", |
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129 file=sys.stderr, |
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130 ) |
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131 exit(1) |
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132 elif args.primer_file is not None and args.artic_primers is not None: |
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133 print( |
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134 "Only one of --artic_primers or --primer_file + --primer_name + --primer_description can be chosen" |
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135 ) |
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136 exit(1) |
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137 |
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138 config = json.load(open(args.galaxy_datamanager_filename)) |
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139 output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) |
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140 if output_directory is None: |
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141 output_directory = args.output_directory |
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142 |
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143 if not os.path.isdir(output_directory): |
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144 os.makedirs(output_directory) |
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145 |
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146 data_manager_dict = {} |
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147 data_manager_dict["data_tables"] = json.load( |
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148 open(args.galaxy_datamanager_filename) |
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149 ).get("data_tables", {}) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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150 data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {}) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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151 data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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152 "data_tables" |
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153 ].get(DATA_TABLE_NAME, []) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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154 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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155 if args.artic_primers: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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156 data = fetch_artic_primers(output_directory, args.artic_primers) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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157 else: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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158 data = install_primer_file( |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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159 output_directory, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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160 args.primer_file, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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161 args.primer_name, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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162 args.primer_description, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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163 ) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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164 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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165 data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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166 print(data_manager_dict) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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167 json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w")) |