details: http://www.bx.psu.edu/hg/galaxy/rev/ba2412c2a4d9 changeset: 2659:ba2412c2a4d9 user: guru date: Wed Sep 02 13:36:16 2009 -0400 description: Added a new option to 'fetch closest features' tool to return the closest feature either upstream or downstream. 3 file(s) affected in this change: test-data/closest_features_either.interval tools/new_operations/flanking_features.py tools/new_operations/flanking_features.xml diffs (524 lines): diff -r 0cb12b9d9d4d -r ba2412c2a4d9 test-data/closest_features_either.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features_either.interval Wed Sep 02 13:36:16 2009 -0400 @@ -0,0 +1,424 @@ +chr22 30128507 30133507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 30136507 30141507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30132507 30137507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 30140507 30145507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30136507 30141507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 30128507 30133507 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uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31740507 31745507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31732507 31737507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31744507 31749507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31736507 31741507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31748507 31753507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31740507 31745507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31752507 31757507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31744507 31749507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31756507 31761507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31748507 31753507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31760507 31765507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31752507 31757507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31764507 31769507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31756507 31761507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31768507 31773507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31760507 31765507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31772507 31777507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31764507 31769507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31776507 31781507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31768507 31773507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31780507 31785507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31772507 31777507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31784507 31789507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31776507 31781507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31788507 31793507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31780507 31785507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31792507 31797507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31784507 31789507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31796507 31801507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31788507 31793507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31800507 31805507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31792507 31797507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31804507 31809507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31796507 31801507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31808507 31813507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31800507 31805507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31812507 31817507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31804507 31809507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31816507 31821507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31808507 31813507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31820507 31825507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31812507 31817507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + diff -r 0cb12b9d9d4d -r ba2412c2a4d9 tools/new_operations/flanking_features.py --- a/tools/new_operations/flanking_features.py Tue Sep 01 17:01:44 2009 -0400 +++ b/tools/new_operations/flanking_features.py Wed Sep 02 13:36:16 2009 -0400 @@ -62,12 +62,16 @@ def proximal_region_finder(readers, region, comments=True): primary = readers[0] features = readers[1] + either = False if region == 'Upstream': up, down = True, False elif region == 'Downstream': up, down = False, True else: up, down = True, True + if region == 'Either': + either = True + # Read features into memory: rightTree = quicksect.IntervalTree() for item in features: @@ -107,14 +111,29 @@ res_ind = ends.index(max(ends)) #fetch the index of the closest interval i.e. the interval with the max end from the results_up list else: res_ind = 0 - map(outfields.append, result_up[res_ind].other) - yield outfields + if not(either): + map(outfields.append, result_up[res_ind].other) + yield outfields if result_down: outfields = list(interval) - map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval + if not(either): + map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval + yield outfields + + if either: + if result_up and result_down: + if abs(start - int(result_up[res_ind].end)) <= abs(end - int(result_down[-1].start)): + map(outfields.append, result_up[res_ind].other) + else: + map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval + elif result_up: + map(outfields.append, result_up[res_ind].other) + else: + map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval yield outfields - + + def main(): options, args = doc_optparse.parse( __doc__ ) try: diff -r 0cb12b9d9d4d -r ba2412c2a4d9 tools/new_operations/flanking_features.xml --- a/tools/new_operations/flanking_features.xml Tue Sep 01 17:01:44 2009 -0400 +++ b/tools/new_operations/flanking_features.xml Wed Sep 02 13:36:16 2009 -0400 @@ -1,10 +1,11 @@ -<tool id="flanking_features_1" name="Fetch closest feature" version="2.0.0"> +<tool id="flanking_features_1" name="Fetch closest feature" version="3.0.0"> <description> for every interval</description> <command interpreter="python">flanking_features.py $input1 $input2 $out_file1 $direction -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command> <inputs> <param format="interval" name="input1" type="data" label="For every interval in"/> - <param format="interval" name="input2" type="data" label="Fetch features from"/> - <param name="direction" type="select" label="Location of the flanking features"> + <param format="interval" 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> @@ -14,13 +15,19 @@ <data format="interval" name="out_file1" /> </outputs> <tests> - <test> - <param name="input1" value="4_windows.bed"/> + <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> + </test> + <test> <param name="input1" value="4_windows.bed"/> <param name="input2" value="4_windows_2.bed"/> <param name="direction" value="Upstream"/>