# HG changeset patch # User bgruening # Date 1567004125 14400 # Node ID d150ac3d853d7127581aeb33398a74c8a0997ec6 # Parent 750c1684d47cffb0c575397499475a4f83077559 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 06ffe450bafa280eee8a4331c9cfc9e1ece7c522" diff -r 750c1684d47c -r d150ac3d853d split_file_to_collection.py --- a/split_file_to_collection.py Mon Feb 18 15:20:56 2019 -0500 +++ b/split_file_to_collection.py Wed Aug 28 10:55:25 2019 -0400 @@ -15,6 +15,7 @@ FILETYPES = {'fasta': '^>', 'fastq': '^@', 'tabular': '^.*', + 'txt': '^.*', 'mgf': '^BEGIN IONS'} @@ -37,6 +38,8 @@ ftype = args["ftype"] + assert ftype != "generic" or args["generic_re"] != None, "--generic_re needs to be given for generic input" + if args["ftype"] == "tabular" and args["by"] == "col": args["match"] = replace_mapped_chars(args["match"]) args["sub"] = replace_mapped_chars(args["sub"]) @@ -56,7 +59,8 @@ parser.add_argument('--file_ext', '-e', help="If not splitting by column," + " the extension of the new files (without a period)") parser.add_argument('--ftype', '-f', help="The type of the file to split", required = True, - choices=["mgf", "fastq", "fasta", "tabular"]) + choices=["mgf", "fastq", "fasta", "tabular", "txt", "generic"]) + parser.add_argument('--generic_re', '-g', help="Regular expression indicating the start of a new record (only for generic)", required = False) parser.add_argument('--by', '-b', help="Split by line or by column (tabular only)", default = "row", choices = ["col", "row"]) parser.add_argument('--top', '-t', type=int, default=0, help="Number of header lines to carry over to new files. " + @@ -96,7 +100,7 @@ def split_by_record(args, in_file, out_dir, top, ftype): # get record separator for given filetype - sep = re.compile(FILETYPES[ftype]) + sep = re.compile(FILETYPES.get(ftype, args["generic_re"])) numnew = args["numnew"] diff -r 750c1684d47c -r d150ac3d853d split_file_to_collection.xml --- a/split_file_to_collection.xml Mon Feb 18 15:20:56 2019 -0500 +++ b/split_file_to_collection.xml Wed Aug 28 10:55:25 2019 -0400 @@ -1,6 +1,19 @@ - + to dataset collection + + + + + + + + + + + + + @@ -73,6 +93,8 @@ + + @@ -85,30 +107,10 @@ - - - - - - - - - - - - + + - - - - - - - - - - - + @@ -128,25 +130,44 @@ + + + + + + + + + + + - + split_parms['select_ftype'] == "tabular" - + split_parms['select_ftype'] == "mgf" - + split_parms['select_ftype'] == "fasta" - + split_parms['select_ftype'] == "fastq" + + + split_parms['select_ftype'] == "txt" + + + + split_parms['select_ftype'] == "generic" + @@ -257,21 +278,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .*" for FASTA, or "@.*" for FASTQ. +The tool has presets for text, tabular data sets (which are split by line), FASTA, FASTQ, and MGF. +For other data types the text delimiting records can be specified manually using the generic splitter. + +If splitting by line (or by some other item, like a FASTA entry or an MGF record, the splitting can be either done alternating, in original record order, or at random. + +If t records are to be distributed to n new data sets, then the i-th record goes to data set + +* floor(i / t * n) (for batch), +* i % n (for alternating), or +* a random data set + +For instance, t=5 records are distributed as follows on n=2 data sets + += === === ==== +i bat alt rand += === === ==== +0 0 0 0 +1 0 1 1 +2 0 0 1 +3 1 1 0 +4 1 0 0 += === === ==== + +If the five records are distributed on n=3 data sets: + += === === ==== +i bat alt rand += === === ==== +0 0 0 0 +1 0 1 1 +2 1 2 2 +3 1 0 0 +4 2 1 1 += === === ==== + +Note that there are no guarantees when splitting at random that every result file will be non-empty, so downstream tools should be able to gracefully handle empty files. + If a tabular file is used as input, you may choose to split by line or by column. If split by column, a new file is created for each unique value in the column. In addition, (Python) regular expressions may be used to transform the value in the column to a new value. Caution should be used with this feature, as it could transform all values to the same value, or other unexpected behavior. The default regular expression uses each value in the column without modifying it. - -If splitting by line (or by some other item, like a FASTA entry or an MGF section), the splitting can be either done sequentially or at random. -Note that there are no guarantees when splitting at random that every result file will be non-empty, so downstream tools should be able to gracefully handle empty files. - -**Note** - -Due to current limitations with dataset collections, a log file is produced when running this tool. It will usually be empty, but if the tool fails, any errors will be printed to the log file. ]]> diff -r 750c1684d47c -r d150ac3d853d test-data/3_molecules.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_molecules.sdf Wed Aug 28 10:55:25 2019 -0400 @@ -0,0 +1,350 @@ + + Chemfp + + 21 21 0 0 0 0 0 0 0 0999 V2000 + 1.2333 0.5540 0.7792 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6952 -2.7148 -0.7502 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7958 -2.1843 0.8685 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7813 0.8105 -1.4821 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0857 0.6088 0.4403 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7927 -0.5515 0.1244 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7288 1.8464 0.4133 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1426 -0.4741 -0.2184 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0787 1.9238 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7855 0.7636 -0.2453 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1409 -1.8536 0.1477 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1094 0.6715 -0.3113 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5305 0.5996 0.1635 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1851 2.7545 0.6593 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7247 -1.3605 -0.4564 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5797 2.8872 0.0506 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8374 0.8238 -0.5090 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7290 1.4184 0.8593 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2045 0.6969 -0.6924 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7105 -0.3659 0.6426 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2555 -3.5916 -0.7337 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> +2244 + +> +0.6 + +> +1 +11 +10 +3 +15 +17 +13 +5 +16 +7 +14 +9 +8 +4 +18 +6 +12 +2 + +> +18 +1 -0.23 +10 -0.15 +11 0.63 +12 0.66 +13 0.06 +14 0.15 +15 0.15 +16 0.15 +17 0.15 +2 -0.65 +21 0.5 +3 -0.57 +4 -0.57 +5 0.08 +6 0.09 +7 -0.15 +8 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0 0 0 0 0 0 0 0 0 0 + 3.7290 1.4184 0.8593 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2045 0.6969 -0.6924 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7105 -0.3659 0.6426 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2555 -3.5916 -0.7337 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +$$$$ diff -r 750c1684d47c -r d150ac3d853d test-data/mol_0.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mol_0.sdf Wed Aug 28 10:55:25 2019 -0400 @@ -0,0 +1,350 @@ + + Chemfp + + 21 21 0 0 0 0 0 0 0 0999 V2000 + 1.2333 0.5540 0.7792 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6952 -2.7148 -0.7502 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7958 -2.1843 0.8685 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7813 0.8105 -1.4821 O 0 0 0 0 0 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