Mercurial > repos > earlhaminst > blast_parser

annotate blast_parser.py @ 4:363f3480622d draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
author earlhaminst
date Thu, 12 Oct 2017 07:25:29 -0400
parents 70df762b48a8
children
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70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents:
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1 """
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents:
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2 Simple parser to convert a BLAST 12-column or 24-column tabular output into a
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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3 3-column tabular input for hcluster_hg (id1, id2, weight):
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents:
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4 """
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents:
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5 import argparse
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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6 import math
4
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
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7 import sqlite3
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
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8 import tempfile
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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10 BATCH_SIZE = 2000
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
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13 def create_tables(conn):
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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14 cur = conn.cursor()
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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15 cur.execute('''CREATE TABLE alignment (
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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16 id INTEGER PRIMARY KEY,
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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17 sequence1_id VARCHAR NOT NULL,
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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18 sequence2_id VARCHAR NOT NULL,
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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19 weight INTEGER NOT NULL)''')
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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20 conn.commit()
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earlhaminst
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23 def main():
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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24 parser = argparse.ArgumentParser()
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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25 parser.add_argument('-i', metavar='in-file', type=argparse.FileType('rt'), required=True, help='Path to input file')
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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26 parser.add_argument('-o', metavar='out-file', type=argparse.FileType('wt'), required=True, help='Path to output file')
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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27 parser.add_argument('-r', action='store_true', default=False,
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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28 dest='reciprocal',
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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29 help='Annotate homolog pair')
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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30 options = parser.parse_args()
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
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earlhaminst
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32 db_file = tempfile.NamedTemporaryFile(suffix=".sqlite")
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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earlhaminst
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34 conn = sqlite3.connect(db_file.name)
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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35 conn.execute('PRAGMA foreign_keys = ON')
3
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earlhaminst
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37 create_tables(conn)
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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39 cur = conn.cursor()
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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earlhaminst
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41 i = 0
3
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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42 for line in options.i:
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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43 line = line.rstrip()
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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44 line_cols = line.split('\t')
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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45 sequence1_id = line_cols[0]
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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46 sequence2_id = line_cols[1]
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
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47
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48 # Ignore self-matching hits
4
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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49 if sequence1_id == sequence2_id:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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50 continue
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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51
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earlhaminst
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52 i = i + 1
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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53 evalue = float(line_cols[10])
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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54
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earlhaminst
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55 # Convert evalue to an integer weight with max 100
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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56 if evalue != 0.0:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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57 weight = min(100, round(math.log10(evalue) / -2.0))
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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58 else:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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59 # If the evalue is 0, leave weight at 100
3
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60 weight = 100
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61
4
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earlhaminst
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62 cur.execute('INSERT INTO alignment (id, sequence1_id, sequence2_id, weight) VALUES (?, ?, ?, ?)',
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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63 (i, sequence1_id, sequence2_id, weight))
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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64
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earlhaminst
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65 # Commit transaction at every BATCH_SIZE rows to save memory
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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66 if i % BATCH_SIZE == 0:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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67 conn.commit()
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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68 # Commit final transaction
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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69 conn.commit()
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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70 options.i.close()
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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71
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72 # Delete alternative alignments keeping only one with max weight
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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73 cur.execute('DELETE FROM alignment WHERE id NOT IN (SELECT id FROM alignment GROUP BY sequence1_id, sequence2_id HAVING weight=max(weight))')
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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74 conn.commit()
3
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75
4
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76 if options.reciprocal:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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77 query = 'SELECT a1.sequence1_id, a1.sequence2_id, a1.weight FROM alignment a1, alignment a2 WHERE a1.sequence1_id = a2.sequence2_id AND a1.sequence2_id = a2.sequence1_id ORDER BY a1.id'
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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78 else:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
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79 query = 'SELECT sequence1_id, sequence2_id, weight FROM alignment ORDER BY id'
3
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80
4
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81 cur.execute(query)
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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82 while True:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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83 rows = cur.fetchmany(BATCH_SIZE)
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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84 if not rows:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
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85 break
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
diff changeset
86 for row in rows:
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
diff changeset
87 options.o.write("%s\t%s\t%d\n" % row)
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
diff changeset
88
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
diff changeset
89 conn.close()
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
diff changeset
90 db_file.close()
363f3480622d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
earlhaminst
parents: 3
diff changeset
91 options.o.close()
3
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents:
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92
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents:
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93
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents:
diff changeset
94 if __name__ == "__main__":
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents:
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95 main()