Mercurial > repos > bgruening > split_file_to_collection

annotate split_file_to_collection.py @ 4:0850f2dfba13 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
author bgruening
date Wed, 09 Oct 2019 07:34:49 -0400
parents 2ddc36385d7a
children e77b954f0da5
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de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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1 #!/usr/bin/env python
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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3 import argparse
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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4 import os
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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5 import re
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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6 import random
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7 import math
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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8
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10 """
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11 regexes that indicate the *beginning* of a record
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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12 new file types can be added by appending to this dict,
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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13 updating the parser, and adding a new type option in the Galaxy wrapper
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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14 """
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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15 FILETYPES = {'fasta': '^>',
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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16 'fastq': '^@',
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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17 'tabular': '^.*',
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18 'txt': '^.*',
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19 'mgf': '^BEGIN IONS',
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20 'sdf': '\$\$\$\$',
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21 }
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24 def main():
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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25 ps = parser_cli()
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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26 args = vars(ps.parse_args())
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28 # get args and validate
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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29 in_file = args["in"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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30 if not os.path.isfile(args["in"]):
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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31 raise FileNotFoundError('Input file does not exist')
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33 out_dir = args["out_dir"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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34 if not os.path.isdir(args["out_dir"]):
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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35 raise FileNotFoundError('out_dir is not a directory')
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37 top = args["top"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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38 if top < 0:
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39 raise ValueError("Number of header lines cannot be negative")
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41 ftype = args["ftype"]
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42
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43 assert ftype != "generic" or args["generic_re"] != None, "--generic_re needs to be given for generic input"
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44
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45 if args["ftype"] == "tabular" and args["by"] == "col":
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46 args["match"] = replace_mapped_chars(args["match"])
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47 args["sub"] = replace_mapped_chars(args["sub"])
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48 split_by_column(args, in_file, out_dir, top)
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50 else:
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51 split_by_record(args, in_file, out_dir, top, ftype)
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54 def parser_cli():
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55 parser = argparse.ArgumentParser(description="split a file into multiple files. " +
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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56 "Can split on the column of a tabular file, " +
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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57 "with custom and useful names based on column value.")
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58 parser.add_argument('--in', '-i', required=True, help="The input file")
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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59 parser.add_argument('--out_dir', '-o', default=os.getcwd(), help="The output directory", required=True)
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60 parser.add_argument('--file_names', '-a', help="If not splitting by column, the base name of the new files")
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61 parser.add_argument('--file_ext', '-e', help="If not splitting by column," +
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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62 " the extension of the new files (without a period)")
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63 parser.add_argument('--ftype', '-f', help="The type of the file to split", required = True,
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64 choices=["mgf", "fastq", "fasta", "sdf", "tabular", "txt", "generic"])
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65 parser.add_argument('--generic_re', '-g', help="Regular expression indicating the start of a new record (only for generic)", required = False)
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66 parser.add_argument('--by', '-b', help="Split by line or by column (tabular only)",
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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67 default = "row", choices = ["col", "row"])
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68 parser.add_argument('--top', '-t', type=int, default=0, help="Number of header lines to carry over to new files. " +
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69 "(tabular only).")
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70 parser.add_argument('--rand', '-r', help="Divide records randomly into new files", action='store_true')
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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71 parser.add_argument('--seed', '-x', help="Provide a seed for the random number generator. " +
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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72 "If not provided and args[\"rand\"]==True, then date is used", type=int)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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73 parser.add_argument('--numnew', '-n', type=int, default = 1,
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74 help="Number of output files desired. Not valid for splitting on a column. Not compatible with chunksize and will be ignored if both are set.")
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75 parser.add_argument('--chunksize', '-k', type=int, default = 0,
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76 help="Number of records by file. Not valid for splitting on a column")
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77 parser.add_argument('--batch', action='store_true',
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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78 help="Distribute files to collection while maintaining order. Ignored if splitting on column.")
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79 parser.add_argument('--split_after', '-p', action='store_true',
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80 help="Split between records after separator (default is before)." +
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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81 "Only for generic - specific ftypes are always split in the default way")
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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82 bycol = parser.add_argument_group('If splitting on a column')
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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83 bycol.add_argument('--match', '-m', default = "(.*)", help="The regular expression to match id column entries")
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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84 bycol.add_argument('--sub', '-s', default = r'\1',
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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85 help="The regular expression to substitute in for the matched pattern.")
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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86 bycol.add_argument('--id_column', '-c', default="1",
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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87 help="Column that is used to name output files. Indexed starting from 1.", type=int)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
88 return parser
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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89
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
90
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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91 def close_files(file_list):
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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92 # finally, close all files
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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93 for open_file in file_list:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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94 open_file.close()
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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95
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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96
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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97 def replace_mapped_chars(pattern):
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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98 """
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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99 handles special escaped characters when coming from galaxy
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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100 """
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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101 mapped_chars = {'\'': '__sq__', '\\': '__backslash__'}
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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102 for key, value in mapped_chars.items():
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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103 pattern = pattern.replace(value, key)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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104 return pattern
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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105
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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106
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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107 def split_by_record(args, in_file, out_dir, top, ftype):
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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108 # get record separator for given filetype
2
d150ac3d853d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 06ffe450bafa280eee8a4331c9cfc9e1ece7c522"
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109 sep = re.compile(FILETYPES.get(ftype, args["generic_re"]))
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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110
4
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111 chunksize = args["chunksize"]
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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112 numnew = args["numnew"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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113
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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114 # random division
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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115 rand = args["rand"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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116 seed = args["seed"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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117 if seed:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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118 random.seed(seed)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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119 else:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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120 random.seed()
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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121
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
122 # batched division (maintains order)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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123 batch = args["batch"]
4
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124
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125
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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126 if chunksize != 0 or batch: # needs to be calculated if either batch or chunksize are selected
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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127 # define n_per_file so we don't get a warning about ref before assignment
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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128 n_per_file = math.inf
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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129
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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130 # number of records
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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131 with open(in_file) as f:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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132 i = 0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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133 for line in f:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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134 if re.match(sep, line) is not None:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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parents:
diff changeset
135 i+=1
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
136 n_records = i + 1
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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137 if top:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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138 n_records -= top # don't count the top lines
4
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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139
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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140 if chunksize == 0: # i.e. no chunking
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
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diff changeset
141 # approx. number of lines per file
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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diff changeset
142 n_per_file = n_records // numnew
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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143 else:
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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144 # approx. number of lines per file
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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145 numnew = n_records // chunksize
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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146 n_per_file = chunksize
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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147
4
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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148
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
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149
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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150
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
151 # make new files
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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152 # strip extension of old file and add number
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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153 custom_new_file_name = args["file_names"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
154 custom_new_file_ext = "." + args["file_ext"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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155 if custom_new_file_name is None:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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parents:
diff changeset
156 new_file_base = os.path.splitext(os.path.basename(in_file))
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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157 else:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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158 new_file_base = [custom_new_file_name, custom_new_file_ext]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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159
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
160 newfiles = [
3
2ddc36385d7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 8d069684e155d2f5b6fae06d14d98ce41321da53"
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161 open(os.path.join(out_dir, "%s_%06d%s" % (new_file_base[0], count, new_file_base[1])) , "w")
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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162 for count in range(0, numnew)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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163 ]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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164
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
165 # bunch o' counters
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
166 # index to list of new files
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
167 new_file_counter = 0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
168
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
169 # used for top
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
170 # number of lines read so far
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
171 n_read = 0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
172 # to contain header specified by top
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
173 header = ""
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
174 # keep track of the files that have been opened so far
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
175 fresh_files = {i for i in range(0, numnew)}
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
176
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
177 # keep track in loop of number of records in each file
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
178 # only used in batch
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
179 records_in_file = 0
3
2ddc36385d7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 8d069684e155d2f5b6fae06d14d98ce41321da53"
bgruening
parents: 2
diff changeset
180
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
181 # open file
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
182 with open(in_file, "r") as file:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
183 record = ""
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
184 for line in file:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
185 n_read += 1
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
186 if n_read <= top:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
187 header += line
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
188 continue
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
189 # check if beginning of line is record sep
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
190 # if beginning of line is record sep, either start record or finish one
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
191 if re.match(sep, line) is not None:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
192 # this only happens first time through
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
193 if record == "":
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
194 record += line
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
195 else:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
196 # if is in fresh_files, write header and drop from freshFiles
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
197 if new_file_counter in fresh_files:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
198 newfiles[new_file_counter].write(header)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
199 fresh_files.remove(new_file_counter)
4
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
200
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
201 if ftype != "sdf" and args["split_after"] == False:
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
202 # write record to file
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
203 newfiles[new_file_counter].write(record)
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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diff changeset
204
4
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
205 # if not the first time through, we assign the new record
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
206 record = line
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
207
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
208 else: # for sdf we want to write the line to the record before starting a new one
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
209 record += line
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
210 newfiles[new_file_counter].write(record)
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
211 record = ""
0850f2dfba13 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"
bgruening
parents: 3
diff changeset
212
0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
213 # change destination file
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
214 if rand:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
215 new_file_counter = int(math.floor(random.random() * numnew))
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
216 elif batch:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
217 # number of records read per file
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
218 records_in_file += 1
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
219 # have we reached the max for each file?
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
220 # if so, switch file
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
221 if records_in_file >= n_per_file:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
222 new_file_counter = (new_file_counter + 1) % numnew
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
223 records_in_file = 0 # reset to 0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
224 else:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
225 new_file_counter = (new_file_counter + 1) % numnew
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
226 # if beginning of line is not record sep, we must be inside a record
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
227 # so just append
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
228 else:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
229 record += line
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
230 # after loop, write final record to file
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
231 newfiles[new_file_counter].write(record)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
232 # close new files
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
233 close_files(newfiles)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
234
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
235
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
236 def split_by_column(args, in_file, out_dir, top):
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
237
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
238 # shift to 0-based indexing
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
239 id_col = int(args["id_column"]) - 1
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
240
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
241 try:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
242 match = re.compile(args["match"])
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
243 except re.error:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
244 print("ERROR: Match (-m) supplied is not valid regex.")
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
245 raise
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
246
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
247 sub = args["sub"]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
248
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
249 # set of file names
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
diff changeset
250 new_files = dict()
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
bgruening
parents:
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251
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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252 # keep track of how many lines have been read
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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253 n_read = 0
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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254 header = ""
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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255 with open(in_file) as file:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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256 for line in file:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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257 # if still in top, save to header
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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258 n_read += 1
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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259 if n_read <= top:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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260 header += line
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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261 continue
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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262 # split into columns, on tab
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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263 fields = re.split(r'\t', line.strip('\n'))
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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264
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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265 # get id column value
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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266 id_col_val = fields[id_col]
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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267
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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268 # use regex to get new file name
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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269 out_file_name = re.sub(match, sub, id_col_val)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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270 out_file_path = os.path.join(out_dir, out_file_name)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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271
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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272 # write
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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273 if out_file_name not in new_files.keys():
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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274 # open file (new, so not already open)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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275 current_new_file = open(out_file_path, "w")
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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276 current_new_file.write(header)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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277 current_new_file.write(line)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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278 # add to dict
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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279 new_files[out_file_name] = current_new_file
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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280 else:
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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281 # file is already open, so just write to it
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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282 new_files[out_file_name].write(line)
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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283
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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284 # finally, close all files
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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285 close_files(new_files.values())
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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286
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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287
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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288 if __name__ == "__main__":
de3c2c88e710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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289 main()