| Next changeset 1:8307665c4b6c (2015-11-11) |
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Commit message:
Imported from capsule None |
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added:
flanking_features.py flanking_features.xml test-data/4_windows.bed test-data/4_windows.gff test-data/4_windows_2.bed test-data/4_windows_2.gff test-data/4_windows_3.bed test-data/closest_features.interval test-data/closest_features_both.gff test-data/closest_features_both.interval test-data/closest_features_both2.gff test-data/closest_features_down.interval test-data/closest_features_either.interval test-data/closest_features_up.interval tool_dependencies.xml utils/__init__.py utils/gff_util.py utils/odict.py |
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| diff -r 000000000000 -r 90100b587723 flanking_features.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flanking_features.py Tue Apr 01 10:52:59 2014 -0400 |
| [ |
| b'@@ -0,0 +1,212 @@\n+#!/usr/bin/env python\n+#By: Guruprasad Ananda\n+"""\n+Fetch closest up/downstream interval from features corresponding to every interval in primary\n+\n+usage: %prog primary_file features_file out_file direction\n+ -1, --cols1=N,N,N,N: Columns for start, end, strand in first file\n+ -2, --cols2=N,N,N,N: Columns for start, end, strand in second file\n+ -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval\n+ -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval\n+"""\n+\n+import sys, traceback, fileinput\n+from warnings import warn\n+from bx.cookbook import doc_optparse\n+from galaxy.tools.util.galaxyops import *\n+from bx.intervals.io import *\n+from bx.intervals.operations import quicksect\n+from utils.gff_util import *\n+\n+assert sys.version_info[:2] >= ( 2, 4 )\n+\n+def get_closest_feature (node, direction, threshold_up, threshold_down, report_func_up, report_func_down):\n+ #direction=1 for +ve strand upstream and -ve strand downstream cases; and it is 0 for +ve strand downstream and -ve strand upstream cases\n+ #threhold_Up is equal to the interval start for +ve strand, and interval end for -ve strand\n+ #threhold_down is equal to the interval end for +ve strand, and interval start for -ve strand\n+ if direction == 1: \n+ if node.maxend <= threshold_up:\n+ if node.end == node.maxend:\n+ report_func_up(node)\n+ elif node.right and node.left:\n+ if node.right.maxend == node.maxend:\n+ get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ elif node.left.maxend == node.maxend:\n+ get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ elif node.right and node.right.maxend == node.maxend:\n+ get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ elif node.left and node.left.maxend == node.maxend:\n+ get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ elif node.minend <= threshold_up:\n+ if node.end <= threshold_up:\n+ report_func_up(node)\n+ if node.left and node.right:\n+ if node.right.minend <= threshold_up:\n+ get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ if node.left.minend <= threshold_up:\n+ get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ elif node.left:\n+ if node.left.minend <= threshold_up:\n+ get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ elif node.right:\n+ if node.right.minend <= threshold_up:\n+ get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ elif direction == 0:\n+ if node.start > threshold_down:\n+ report_func_down(node)\n+ if node.left:\n+ get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+ else:\n+ if node.right:\n+ get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)\n+\n+def proximal_region_finder(readers, region, comments=True):\n+ """\n+ Returns an iterator that yields elements of the form [ <original_interval>, <closest_feature> ]. \n+ Intervals are GenomicInterval objects. \n+ """\n+ primary = readers[0]\n+ features = readers[1]\n+ either = False\n+ if region == \'Upstream\':\n+ up, down = True, False\n+ e'..b't_up[res_ind].end)) <= abs(end - int(result_down[-1].start)):\n+ iter_val = [ interval, result_up[res_ind].other ]\n+ else:\n+ #The last element of result_down will be the closest element to the given interval\n+ iter_val = [ interval, result_down[-1].other ]\n+ elif result_up:\n+ iter_val = [ interval, result_up[res_ind].other ]\n+ elif result_down:\n+ #The last element of result_down will be the closest element to the given interval\n+ iter_val = [ interval, result_down[-1].other ]\n+ yield iter_val\n+ \n+def main():\n+ options, args = doc_optparse.parse( __doc__ )\n+ try:\n+ chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )\n+ chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )\n+ in1_gff_format = bool( options.gff1 )\n+ in2_gff_format = bool( options.gff2 )\n+ in_fname, in2_fname, out_fname, direction = args\n+ except:\n+ doc_optparse.exception()\n+ \n+ # Set readers to handle either GFF or default format.\n+ if in1_gff_format:\n+ in1_reader_wrapper = GFFIntervalToBEDReaderWrapper\n+ else:\n+ in1_reader_wrapper = NiceReaderWrapper\n+ if in2_gff_format:\n+ in2_reader_wrapper = GFFIntervalToBEDReaderWrapper\n+ else:\n+ in2_reader_wrapper = NiceReaderWrapper\n+\n+ g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ),\n+ chrom_col=chr_col_1,\n+ start_col=start_col_1,\n+ end_col=end_col_1,\n+ strand_col=strand_col_1,\n+ fix_strand=True )\n+ g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),\n+ chrom_col=chr_col_2,\n+ start_col=start_col_2,\n+ end_col=end_col_2,\n+ strand_col=strand_col_2,\n+ fix_strand=True )\n+\n+ # Find flanking features.\n+ out_file = open( out_fname, "w" )\n+ try:\n+ for result in proximal_region_finder([g1,g2], direction):\n+ if type( result ) is list:\n+ line, closest_feature = result\n+ # Need to join outputs differently depending on file types.\n+ if in1_gff_format:\n+ # Output is GFF with added attribute \'closest feature.\'\n+\n+ # Invervals are in BED coordinates; need to convert to GFF.\n+ line = convert_bed_coords_to_gff( line )\n+ closest_feature = convert_bed_coords_to_gff( closest_feature )\n+ \n+ # Replace double quotes with single quotes in closest feature\'s attributes.\n+ out_file.write( "%s closest_feature \\"%s\\" \\n" % \n+ ( "\\t".join( line.fields ), \\\n+ "\\t".join( closest_feature.fields ).replace( "\\"", "\\\\\\"" )\n+ ) )\n+ else:\n+ # Output is BED + closest feature fields.\n+ output_line_fields = []\n+ output_line_fields.extend( line.fields )\n+ output_line_fields.extend( closest_feature.fields )\n+ out_file.write( "%s\\n" % ( "\\t".join( output_line_fields ) ) )\n+ else:\n+ out_file.write( "%s\\n" % result )\n+ except ParseError, exc:\n+ fail( "Invalid file format: %s" % str( exc ) )\n+\n+ print "Direction: %s" %(direction)\n+ if g1.skipped > 0:\n+ print skipped( g1, filedesc=" of 1st dataset" )\n+ if g2.skipped > 0:\n+ print skipped( g2, filedesc=" of 2nd dataset" )\n+\n+if __name__ == "__main__":\n+ main()\n' |
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| diff -r 000000000000 -r 90100b587723 flanking_features.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flanking_features.xml Tue Apr 01 10:52:59 2014 -0400 |
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| @@ -0,0 +1,131 @@ +<tool id="flanking_features_1" name="Fetch closest non-overlapping feature" version="4.0.1"> + <description> for every interval</description> + <requirements> + <requirement type="package" version="0.7.1">bx-python</requirement> + <requirement type="package" version="1.0.0">galaxy-ops</requirement> + </requirements> + <command interpreter="python"> + flanking_features.py $input1 $input2 $out_file1 $direction + + #if isinstance( $input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): + -1 1,4,5,7 --gff1 + #else: + -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} + #end if + + #if isinstance( $input2.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): + -2 1,4,5,7 --gff2 + #else: + -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} + #end if + </command> + <inputs> + <param format="interval,gff" name="input1" type="data" label="For every interval in"/> + <param format="interval,gff" name="input2" type="data" label="Fetch closest feature(s) from"/> + <param name="direction" type="select" label="Located"> + <option value="Either">Either Upstream or Downstream</option> + <option value="Both">Both Upstream and Downstream</option> + <option value="Upstream">Upstream</option> + <option value="Downstream">Downstream</option> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="4_windows.bed"/> + <param name="input2" value="4_windows_2.bed"/> + <param name="direction" value="Either"/> + <output name="out_file1" file="closest_features_either.interval"/> + </test> + <test> + <param name="input1" value="4_windows.bed"/> + <param name="input2" value="4_windows_2.bed"/> + <param name="direction" value="Both"/> + <output name="out_file1" file="closest_features.interval"/> + </test> + <test> + <param name="input1" value="4_windows.bed"/> + <param name="input2" value="4_windows_2.bed"/> + <param name="direction" value="Upstream"/> + <output name="out_file1" file="closest_features_up.interval"/> + </test> + <test> + <param name="input1" value="4_windows.bed"/> + <param name="input2" value="4_windows_2.bed"/> + <param name="direction" value="Downstream"/> + <output name="out_file1" file="closest_features_down.interval"/> + </test> + <test> + <param name="input1" value="4_windows.bed"/> + <param name="input2" value="4_windows_3.bed"/> + <param name="direction" value="Both"/> + <output name="out_file1" file="closest_features_both.interval"/> + </test> + <!-- Tests for GFF functionality. --> + + <test> + <param name="input1" value="4_windows.bed"/> + <param name="input2" value="4_windows_2.gff"/> + <param name="direction" value="Either"/> + <output name="out_file1" file="closest_features_both.gff"/> + </test> + <test> + <param name="input1" value="4_windows.gff"/> + <param name="input2" value="4_windows_2.gff"/> + <param name="direction" value="Either"/> + <output name="out_file1" file="closest_features_both2.gff"/> + </test> + + </tests> + <help> + +.. class:: infomark + +**What it does** + +For every interval in the **interval** dataset, this tool fetches the **closest non-overlapping** upstream and / or downstream features from the **features** dataset. + +----- + +.. class:: warningmark + +**Note:** + +Every line should contain at least 3 columns: chromosome number, start and stop coordinates. If any of these columns is missing or if start and stop coordinates are not numerical, the lines will be treated as invalid and skipped. The number of skipped lines is documented in the resulting history item as a "data issue". + +If the strand column is missing from your input interval dataset, the intervals will be considered to be on positive strand. You can add a strand column to your input dataset by using the *Text Manipulation->Add column* tool. + +For GFF files, features are added as a GTF-style attribute at the end of the line. + +----- + +**Example** + +If the **intervals** are:: + + chr1 10 100 Query1.1 + chr1 500 1000 Query1.2 + chr1 1100 1250 Query1.3 + +and the **features** are:: + + chr1 120 180 Query2.1 + chr1 140 200 Query2.2 + chr1 580 1050 Query2.3 + chr1 2000 2204 Query2.4 + chr1 2500 3000 Query2.5 + +Running this tool for **Both Upstream and Downstream** will return:: + + chr1 10 100 Query1.1 chr1 120 180 Query2.1 + chr1 500 1000 Query1.2 chr1 140 200 Query2.2 + chr1 500 1000 Query1.2 chr1 2000 2204 Query2.4 + chr1 1100 1250 Query1.3 chr1 580 1050 Query2.3 + chr1 1100 1250 Query1.3 chr1 2000 2204 Query2.4 + +</help> + + +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 90100b587723 test-data/4_windows.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_windows.bed Tue Apr 01 10:52:59 2014 -0400 |
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| b'@@ -0,0 +1,424 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chr22_29227_f\t0\t+\n+chr22\t31604507\t31609507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31608507\t31613507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31612507\t31617507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31616507\t31621507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31620507\t31625507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31624507\t31629507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31628507\t31633507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31632507\t31637507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31636507\t31641507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31640507\t31645507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31644507\t31649507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31648507\t31653507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31652507\t31657507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31656507\t31661507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31660507\t31665507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31664507\t31669507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31668507\t31673507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31672507\t31677507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31676507\t31681507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31680507\t31685507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31684507\t31689507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31688507\t31693507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31692507\t31697507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31696507\t31701507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31700507\t31705507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31704507\t31709507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31708507\t31713507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31712507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31816507\t31821507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31820507\t31825507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/4_windows.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_windows.gff Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,427 @@\n+##gff-version 2\n+##bed_to_gff_converter.py\n+\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30128508\t30133507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30132508\t30137507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30136508\t30141507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30140508\t30145507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30144508\t30149507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30148508\t30153507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30152508\t30157507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30156508\t30161507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30160508\t30165507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30164508\t30169507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30168508\t30173507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30172508\t30177507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30176508\t30181507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30180508\t30185507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30184508\t30189507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30188508\t30193507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30192508\t30197507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30196508\t30201507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30200508\t30205507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30204508\t30209507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30208508\t30213507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30212508\t30217507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30216508\t30221507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30220508\t30225507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30224508\t30229507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30228508\t30233507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30232508\t30237507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30236508\t30241507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30240508\t30245507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30244508\t30249507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30248508\t30253507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30252508\t30257507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30256508\t30261507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30260508\t30265507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30264508\t30269507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30268508\t30273507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30272508\t30277507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gf'..b'_2_0_chr22_29227_f\t31672508\t31677507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31676508\t31681507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31680508\t31685507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31684508\t31689507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31688508\t31693507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31692508\t31697507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31696508\t31701507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31700508\t31705507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31704508\t31709507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31708508\t31713507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31712508\t31717507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31716508\t31721507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31720508\t31725507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31724508\t31729507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31728508\t31733507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31732508\t31737507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31736508\t31741507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31740508\t31745507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31744508\t31749507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31748508\t31753507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31752508\t31757507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31756508\t31761507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31760508\t31765507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31764508\t31769507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31768508\t31773507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31772508\t31777507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31776508\t31781507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31780508\t31785507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31784508\t31789507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31788508\t31793507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31792508\t31797507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31796508\t31801507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31800508\t31805507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31804508\t31809507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31808508\t31813507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31812508\t31817507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31816508\t31821507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31820508\t31825507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/4_windows_2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_windows_2.bed Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,424 @@\n+chr22\t30128507\t30133507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30132507\t30137507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30136507\t30141507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30140507\t30145507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30144507\t30149507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30148507\t30153507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30152507\t30157507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30156507\t30161507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30160507\t30165507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30164507\t30169507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30168507\t30173507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30172507\t30177507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30176507\t30181507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30180507\t30185507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30184507\t30189507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30188507\t30193507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30192507\t30197507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30196507\t30201507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30200507\t30205507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30204507\t30209507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30208507\t30213507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30212507\t30217507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30216507\t30221507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30220507\t30225507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30224507\t30229507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30228507\t30233507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30232507\t30237507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30236507\t30241507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30240507\t30245507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30244507\t30249507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30248507\t30253507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30252507\t30257507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30256507\t30261507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30260507\t30265507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30264507\t30269507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30268507\t30273507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30272507\t30277507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30276507\t30281507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30280507\t30285507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30284507\t30289507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30288507\t30293507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30292507\t30297507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30296507\t30301507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30300507\t30305507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30304507\t30309507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30308507\t30313507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30312507\t30317507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30316507\t30321507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30320507\t30325507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30324507\t30329507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30328507\t30333507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30332507\t30337507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30336507\t30341507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30340507\t30345507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30344507\t30349507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30348507\t30353507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30352507\t30357507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30356507\t30361507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30360507\t30365507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30364507\t30369507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30368507\t30373507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30372507\t30377507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30376507\t30381507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30380507\t30385507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t303845'..b'nx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31568507\t31573507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31572507\t31577507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31576507\t31581507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31580507\t31585507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31584507\t31589507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31588507\t31593507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31592507\t31597507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31596507\t31601507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31600507\t31605507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31604507\t31609507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31608507\t31613507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31612507\t31617507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31616507\t31621507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31620507\t31625507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31624507\t31629507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31628507\t31633507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31632507\t31637507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31636507\t31641507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31640507\t31645507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31644507\t31649507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31648507\t31653507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31652507\t31657507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31656507\t31661507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31660507\t31665507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31664507\t31669507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31668507\t31673507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31672507\t31677507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31676507\t31681507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31680507\t31685507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31684507\t31689507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31688507\t31693507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31692507\t31697507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31696507\t31701507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31700507\t31705507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31704507\t31709507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31708507\t31713507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31712507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31816507\t31821507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31820507\t31825507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/4_windows_2.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_windows_2.gff Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,427 @@\n+##gff-version 2\n+##bed_to_gff_converter.py\n+\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30128508\t30133507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30132508\t30137507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30136508\t30141507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30140508\t30145507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30144508\t30149507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30148508\t30153507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30152508\t30157507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30156508\t30161507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30160508\t30165507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30164508\t30169507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30168508\t30173507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30172508\t30177507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30176508\t30181507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30180508\t30185507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30184508\t30189507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30188508\t30193507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30192508\t30197507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30196508\t30201507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30200508\t30205507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30204508\t30209507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30208508\t30213507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30212508\t30217507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30216508\t30221507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30220508\t30225507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30224508\t30229507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30228508\t30233507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30232508\t30237507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30236508\t30241507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30240508\t30245507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30244508\t30249507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30248508\t30253507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30252508\t30257507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30256508\t30261507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30260508\t30265507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30264508\t30269507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30268508\t30273507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30272508\t30277507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gf'..b'_2_0_chr22_29227_f\t31672508\t31677507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31676508\t31681507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31680508\t31685507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31684508\t31689507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31688508\t31693507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31692508\t31697507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31696508\t31701507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31700508\t31705507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31704508\t31709507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31708508\t31713507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31712508\t31717507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31716508\t31721507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31720508\t31725507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31724508\t31729507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31728508\t31733507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31732508\t31737507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31736508\t31741507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31740508\t31745507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31744508\t31749507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31748508\t31753507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31752508\t31757507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31756508\t31761507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31760508\t31765507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31764508\t31769507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31768508\t31773507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31772508\t31777507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31776508\t31781507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31780508\t31785507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31784508\t31789507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31788508\t31793507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31792508\t31797507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31796508\t31801507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31800508\t31805507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31804508\t31809507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31808508\t31813507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31812508\t31817507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31816508\t31821507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31820508\t31825507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/4_windows_3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_windows_3.bed Tue Apr 01 10:52:59 2014 -0400 |
| b |
| @@ -0,0 +1,4 @@ +chr22 30127507 30128507 +chr22 30133507 30136507 +chr22 30139507 30140507 +chr22 30145507 30146507 |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/closest_features.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features.interval Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,844 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|
| b |
| diff -r 000000000000 -r 90100b587723 test-data/closest_features_both.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features_both.gff Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,424 @@\n+chr22\t30128507\t30133507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30136507\t30141507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30132507\t30137507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30140507\t30145507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30136507\t30141507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30128507\t30133507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30140507\t30145507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30132507\t30137507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30144507\t30149507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30136507\t30141507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30148507\t30153507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30140507\t30145507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30152507\t30157507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30144507\t30149507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30156507\t30161507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30148507\t30153507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30160507\t30165507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30152507\t30157507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30164507\t30169507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30156507\t30161507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30168507\t30173507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30160507\t30165507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30172507\t30177507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30164507\t30169507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30176507\t30181507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30168507\t30173507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30180507\t30185507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30172507\t30177507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30184507\t30189507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30176507\t30181507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30188507\t30193507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30180507\t30185507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30192507\t30197507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30184507\t30189507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30196507\t30201507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30188507\t30193507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30200507\t30205507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30192507\t30197507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30204507\t30209507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30196507\t30201507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30208507\t30213507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30200507\t30205507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30212507\t30217507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30204507\t30209507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30216507\t30221507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30208507\t30213507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t30220507\t30225507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30212507\t30217507\t0\t+\t.\tuc003bn'..b'728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31720507\t31725507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31724507\t31729507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31728507\t31733507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31732507\t31737507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31736507\t31741507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31740507\t31745507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31744507\t31749507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31748507\t31753507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31752507\t31757507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31756507\t31761507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31760507\t31765507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31764507\t31769507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31768507\t31773507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31772507\t31777507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31776507\t31781507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31780507\t31785507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31784507\t31789507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31788507\t31793507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31792507\t31797507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31796507\t31801507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31800507\t31805507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31804507\t31809507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31816507\t31821507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31808507\t31813507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n+chr22\t31820507\t31825507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31812507\t31817507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;\n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/closest_features_both.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features_both.interval Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,428 @@\n+chr22\t30128507\t30133507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30127507\t30128507\n+chr22\t30128507\t30133507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30133507\t30136507\n+chr22\t30132507\t30137507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30127507\t30128507\n+chr22\t30132507\t30137507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30139507\t30140507\n+chr22\t30136507\t30141507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30133507\t30136507\n+chr22\t30136507\t30141507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30140507\t30145507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30139507\t30140507\n+chr22\t30140507\t30145507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30144507\t30149507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30139507\t30140507\n+chr22\t30148507\t30153507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30152507\t30157507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30156507\t30161507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30160507\t30165507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30164507\t30169507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30168507\t30173507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30172507\t30177507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30176507\t30181507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30180507\t30185507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30184507\t30189507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30188507\t30193507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30192507\t30197507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30196507\t30201507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30200507\t30205507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30204507\t30209507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30208507\t30213507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30212507\t30217507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30216507\t30221507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30220507\t30225507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30224507\t30229507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30228507\t30233507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30232507\t30237507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30236507\t30241507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30240507\t30245507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30244507\t30249507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30248507\t30253507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30252507\t30257507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30256507\t30261507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30260507\t30265507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30264507\t30269507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30268507\t30273507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30272507\t30277507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30276507\t30281507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30280507\t30285507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30284507\t30289507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30288507\t30293507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30292507\t30297507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t30296507\t30301507\t'..b'_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31640507\t31645507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31644507\t31649507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31648507\t31653507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31652507\t31657507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31656507\t31661507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31660507\t31665507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31664507\t31669507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31668507\t31673507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31672507\t31677507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31676507\t31681507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31680507\t31685507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31684507\t31689507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31688507\t31693507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31692507\t31697507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31696507\t31701507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31700507\t31705507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31704507\t31709507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31708507\t31713507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31712507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31816507\t31821507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n+chr22\t31820507\t31825507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30145507\t30146507\n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/closest_features_both2.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features_both2.gff Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,427 @@\n+##gff-version 2\n+##bed_to_gff_converter.py\n+#\n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30128508\t30133507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30136508\t30141507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30132508\t30137507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30140508\t30145507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30136508\t30141507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30128508\t30133507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30140508\t30145507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30132508\t30137507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30144508\t30149507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30136509\t30141507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30148508\t30153507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30140509\t30145507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30152508\t30157507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30144508\t30149507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30156508\t30161507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30148508\t30153507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30160508\t30165507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30152508\t30157507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30164508\t30169507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30156508\t30161507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30168508\t30173507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30160508\t30165507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30172508\t30177507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30164508\t30169507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30176508\t30181507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30168508\t30173507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30180508\t30185507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30172508\t30177507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30184508\t30189507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30176508\t30181507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30188508\t30193507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30180508\t30185507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30192508\t30197507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t30184508\t30189507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.'..b'3bnx.1_cds_2_0_chr22_29227_f\t31744508\t31749507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31756508\t31761507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31748508\t31753507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31760508\t31765507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31752508\t31757507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31764508\t31769507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31756508\t31761507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31768508\t31773507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31760508\t31765507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31772508\t31777507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31764508\t31769507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31776508\t31781507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31768508\t31773507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31780508\t31785507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31772508\t31777507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31784508\t31789507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31776508\t31781507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31788508\t31793507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31780508\t31785507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31792508\t31797507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31784508\t31789507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31796508\t31801507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31788508\t31793507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31800508\t31805507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31792508\t31797507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31804508\t31809507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31796508\t31801507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31808508\t31813507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31800508\t31805507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31812508\t31817507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31804508\t31809507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31816508\t31821507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31808508\t31813507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n+chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31820508\t31825507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f; closest_feature "chr22\tbed2gff\tuc003bnx.1_cds_2_0_chr22_29227_f\t31812508\t31817507\t0\t+\t.\tuc003bnx.1_cds_2_0_chr22_29227_f;" \n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/closest_features_down.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features_down.interval Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,422 @@\n+chr22\t30128507\t30133507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30136507\t30141507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30132507\t30137507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30140507\t30145507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30136507\t30141507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30144507\t30149507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30140507\t30145507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30148507\t30153507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30144507\t30149507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30152507\t30157507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30148507\t30153507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30156507\t30161507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30152507\t30157507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30160507\t30165507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30156507\t30161507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30164507\t30169507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30160507\t30165507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30168507\t30173507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30164507\t30169507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30172507\t30177507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30168507\t30173507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30176507\t30181507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30172507\t30177507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30180507\t30185507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30176507\t30181507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30184507\t30189507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30180507\t30185507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30188507\t30193507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30184507\t30189507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30192507\t30197507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30188507\t30193507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30196507\t30201507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30192507\t30197507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30200507\t30205507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30196507\t30201507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30204507\t30209507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30200507\t30205507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30208507\t30213507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30204507\t30209507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30212507\t30217507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30208507\t30213507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30216507\t30221507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30212507\t30217507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30220507\t30225507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30216507\t30221507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30224507\t30229507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30220507\t30225507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30228507\t30233507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30224507\t30229507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30232507\t30237507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30228507\t30233507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30236507\t30241507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30232507\t30237507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30240507\t30245507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30236507\t30241507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30244507\t30249507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30240507\t30245507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30248507\t30253507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30244507\t30249507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30252507\t30257507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30248507\t30253507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30256507\t30261507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30252507\t30257507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t30260507\t30265507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t30256507\t30261507\tuc003bnx.1_cds_2_0_c'..b'+\tchr22\t31692507\t31697507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31688507\t31693507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31696507\t31701507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31692507\t31697507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31700507\t31705507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31696507\t31701507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31704507\t31709507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31700507\t31705507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31708507\t31713507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31704507\t31709507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31712507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31708507\t31713507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31712507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31816507\t31821507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31820507\t31825507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/closest_features_either.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features_either.interval Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,424 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507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31704507\t31709507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31708507\t31713507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31712507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31816507\t31821507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31820507\t31825507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n' |
| b |
| diff -r 000000000000 -r 90100b587723 test-data/closest_features_up.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features_up.interval Tue Apr 01 10:52:59 2014 -0400 |
| b |
| b'@@ -0,0 +1,422 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507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31704507\t31709507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31708507\t31713507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31712507\t31717507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31716507\t31721507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31720507\t31725507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31724507\t31729507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31728507\t31733507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31732507\t31737507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31736507\t31741507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31740507\t31745507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31744507\t31749507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31748507\t31753507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31752507\t31757507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31756507\t31761507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31760507\t31765507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31764507\t31769507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31768507\t31773507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31772507\t31777507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31776507\t31781507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31780507\t31785507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31784507\t31789507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31788507\t31793507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31792507\t31797507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31796507\t31801507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31800507\t31805507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31804507\t31809507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31816507\t31821507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31808507\t31813507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n+chr22\t31820507\t31825507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\tchr22\t31812507\t31817507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n' |
| b |
| diff -r 000000000000 -r 90100b587723 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 01 10:52:59 2014 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bx-python" version="0.7.1"> + <repository changeset_revision="41eb9d9f667d" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="galaxy-ops" version="1.0.0"> + <repository changeset_revision="4e39032e4ec6" name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
| b |
| diff -r 000000000000 -r 90100b587723 utils/gff_util.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils/gff_util.py Tue Apr 01 10:52:59 2014 -0400 |
| [ |
| b'@@ -0,0 +1,430 @@\n+"""\n+Provides utilities for working with GFF files.\n+"""\n+\n+import copy\n+from bx.intervals.io import *\n+from bx.tabular.io import Header, Comment\n+from utils.odict import odict\n+\n+class GFFInterval( GenomicInterval ):\n+ """\n+ A GFF interval, including attributes. If file is strictly a GFF file,\n+ only attribute is \'group.\'\n+ """\n+ def __init__( self, reader, fields, chrom_col=0, feature_col=2, start_col=3, end_col=4, \\\n+ strand_col=6, score_col=5, default_strand=\'.\', fix_strand=False ):\n+ # HACK: GFF format allows \'.\' for strand but GenomicInterval does not. To get around this,\n+ # temporarily set strand and then unset after initing GenomicInterval.\n+ unknown_strand = False\n+ if not fix_strand and fields[ strand_col ] == \'.\':\n+ unknown_strand = True\n+ fields[ strand_col ] = \'+\'\n+ GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, \\\n+ default_strand, fix_strand=fix_strand )\n+ if unknown_strand:\n+ self.strand = \'.\'\n+ self.fields[ strand_col ] = \'.\'\n+\n+ # Handle feature, score column.\n+ self.feature_col = feature_col\n+ if self.feature_col >= self.nfields:\n+ raise MissingFieldError( "No field for feature_col (%d)" % feature_col )\n+ self.feature = self.fields[ self.feature_col ]\n+ self.score_col = score_col\n+ if self.score_col >= self.nfields:\n+ raise MissingFieldError( "No field for score_col (%d)" % score_col )\n+ self.score = self.fields[ self.score_col ]\n+\n+ # GFF attributes.\n+ self.attributes = parse_gff_attributes( fields[8] )\n+\n+ def copy( self ):\n+ return GFFInterval(self.reader, list( self.fields ), self.chrom_col, self.feature_col, self.start_col,\n+ self.end_col, self.strand_col, self.score_col, self.strand)\n+\n+class GFFFeature( GFFInterval ):\n+ """\n+ A GFF feature, which can include multiple intervals.\n+ """\n+ def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4, \\\n+ strand_col=6, score_col=5, default_strand=\'.\', fix_strand=False, intervals=[], \\\n+ raw_size=0 ):\n+ # Use copy so that first interval and feature do not share fields.\n+ GFFInterval.__init__( self, reader, copy.deepcopy( intervals[0].fields ), chrom_col, feature_col, \\\n+ start_col, end_col, strand_col, score_col, default_strand, \\\n+ fix_strand=fix_strand )\n+ self.intervals = intervals\n+ self.raw_size = raw_size\n+ # Use intervals to set feature attributes.\n+ for interval in self.intervals:\n+ # Error checking. NOTE: intervals need not share the same strand.\n+ if interval.chrom != self.chrom:\n+ raise ValueError( "interval chrom does not match self chrom: %s != %s" % \\\n+ ( interval.chrom, self.chrom ) )\n+ # Set start, end of interval.\n+ if interval.start < self.start:\n+ self.start = interval.start\n+ if interval.end > self.end:\n+ self.end = interval.end\n+\n+ def name( self ):\n+ """ Returns feature\'s name. """\n+ name = None\n+ # Preference for name: GTF, GFF3, GFF.\n+ for attr_name in [\n+ # GTF:\n+ \'gene_id\', \'transcript_id\',\n+ # GFF3:\n+ \'ID\', \'id\',\n+ # GFF (TODO):\n+ \'group\' ]:\n+ name = self.attributes.get( attr_name, None )\n+ if name is not None:\n+ break\n+ return name\n+\n+ def copy( self ):\n+ intervals_copy = []\n+ for interval in self.intervals:\n+ intervals_copy.append( interval.copy() )\n+ '..b' if pair == \'\':\n+ continue\n+ name = pair[0].strip()\n+ if name == \'\':\n+ continue\n+ # Need to strip double quote from values\n+ value = pair[1].strip(" \\"")\n+ attributes[ name ] = value\n+\n+ if len( attributes ) == 0:\n+ # Could not split attributes string, so entire string must be\n+ # \'group\' attribute. This is the case for strictly GFF files.\n+ attributes[\'group\'] = attr_str\n+ return attributes\n+\n+def gff_attributes_to_str( attrs, gff_format ):\n+ """\n+ Convert GFF attributes to string. Supported formats are GFF3, GTF.\n+ """\n+ if gff_format == \'GTF\':\n+ format_string = \'%s "%s"\'\n+ # Convert group (GFF) and ID, parent (GFF3) attributes to transcript_id, gene_id\n+ id_attr = None\n+ if \'group\' in attrs:\n+ id_attr = \'group\'\n+ elif \'ID\' in attrs:\n+ id_attr = \'ID\'\n+ elif \'Parent\' in attrs:\n+ id_attr = \'Parent\'\n+ if id_attr:\n+ attrs[\'transcript_id\'] = attrs[\'gene_id\'] = attrs[id_attr]\n+ elif gff_format == \'GFF3\':\n+ format_string = \'%s=%s\'\n+ attrs_strs = []\n+ for name, value in attrs.items():\n+ attrs_strs.append( format_string % ( name, value ) )\n+ return " ; ".join( attrs_strs )\n+\n+def read_unordered_gtf( iterator, strict=False ):\n+ """\n+ Returns GTF features found in an iterator. GTF lines need not be ordered\n+ or clustered for reader to work. Reader returns GFFFeature objects sorted\n+ by transcript_id, chrom, and start position.\n+ """\n+\n+ # -- Get function that generates line/feature key. --\n+\n+ get_transcript_id = lambda fields: parse_gff_attributes( fields[8] )[ \'transcript_id\' ]\n+ if strict:\n+ # Strict GTF parsing uses transcript_id only to group lines into feature.\n+ key_fn = get_transcript_id\n+ else:\n+ # Use lenient parsing where chromosome + transcript_id is the key. This allows\n+ # transcripts with same ID on different chromosomes; this occurs in some popular\n+ # datasources, such as RefGenes in UCSC.\n+ key_fn = lambda fields: fields[0] + \'_\' + get_transcript_id( fields )\n+\n+\n+ # Aggregate intervals by transcript_id and collect comments.\n+ feature_intervals = odict()\n+ comments = []\n+ for count, line in enumerate( iterator ):\n+ if line.startswith( \'#\' ):\n+ comments.append( Comment( line ) )\n+ continue\n+\n+ line_key = key_fn( line.split(\'\\t\') )\n+ if line_key in feature_intervals:\n+ feature = feature_intervals[ line_key ]\n+ else:\n+ feature = []\n+ feature_intervals[ line_key ] = feature\n+ feature.append( GFFInterval( None, line.split( \'\\t\' ) ) )\n+\n+ # Create features.\n+ chroms_features = {}\n+ for count, intervals in enumerate( feature_intervals.values() ):\n+ # Sort intervals by start position.\n+ intervals.sort( lambda a,b: cmp( a.start, b.start ) )\n+ feature = GFFFeature( None, intervals=intervals )\n+ if feature.chrom not in chroms_features:\n+ chroms_features[ feature.chrom ] = []\n+ chroms_features[ feature.chrom ].append( feature )\n+\n+ # Sort features by chrom, start position.\n+ chroms_features_sorted = []\n+ for chrom_features in chroms_features.values():\n+ chroms_features_sorted.append( chrom_features )\n+ chroms_features_sorted.sort( lambda a,b: cmp( a[0].chrom, b[0].chrom ) )\n+ for features in chroms_features_sorted:\n+ features.sort( lambda a,b: cmp( a.start, b.start ) )\n+\n+ # Yield comments first, then features.\n+ # FIXME: comments can appear anywhere in file, not just the beginning.\n+ # Ideally, then comments would be associated with features and output\n+ # just before feature/line.\n+ for comment in comments:\n+ yield comment\n+\n+ for chrom_features in chroms_features_sorted:\n+ for feature in chrom_features:\n+ yield feature\n+\n' |
| b |
| diff -r 000000000000 -r 90100b587723 utils/odict.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils/odict.py Tue Apr 01 10:52:59 2014 -0400 |
| [ |
| @@ -0,0 +1,85 @@ +""" +Ordered dictionary implementation. +""" + +from UserDict import UserDict + +class odict(UserDict): + """ + http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/107747 + + This dictionary class extends UserDict to record the order in which items are + added. Calling keys(), values(), items(), etc. will return results in this + order. + """ + def __init__( self, dict = None ): + self._keys = [] + UserDict.__init__( self, dict ) + + def __delitem__( self, key ): + UserDict.__delitem__( self, key ) + self._keys.remove( key ) + + def __setitem__( self, key, item ): + UserDict.__setitem__( self, key, item ) + if key not in self._keys: + self._keys.append( key ) + + def clear( self ): + UserDict.clear( self ) + self._keys = [] + + def copy(self): + new = odict() + new.update( self ) + return new + + def items( self ): + return zip( self._keys, self.values() ) + + def keys( self ): + return self._keys[:] + + def popitem( self ): + try: + key = self._keys[-1] + except IndexError: + raise KeyError( 'dictionary is empty' ) + val = self[ key ] + del self[ key ] + return ( key, val ) + + def setdefault( self, key, failobj=None ): + if key not in self._keys: + self._keys.append( key ) + return UserDict.setdefault( self, key, failobj ) + + def update( self, dict ): + for ( key, val ) in dict.items(): + self.__setitem__( key, val ) + + def values( self ): + return map( self.get, self._keys ) + + def iterkeys( self ): + return iter( self._keys ) + + def itervalues( self ): + for key in self._keys: + yield self.get( key ) + + def iteritems( self ): + for key in self._keys: + yield key, self.get( key ) + + def __iter__( self ): + for key in self._keys: + yield key + + def reverse( self ): + self._keys.reverse() + + def insert( self, index, key, item ): + if key not in self._keys: + self._keys.insert( index, key ) + UserDict.__setitem__( self, key, item ) |