flanking_features: flanking_features.py annotate

annotate flanking_features.py @ 3:94248d5b9b8b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

author	devteam
date	Thu, 22 Jun 2017 18:39:31 -0400
parents	850c05b9af00
children

rev	line source
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	1 #!/usr/bin/env python
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	2 # By: Guruprasad Ananda
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	3 """
e928e029f6eb Imported from capsule None devteam parents: diff changeset	4 Fetch closest up/downstream interval from features corresponding to every interval in primary
e928e029f6eb Imported from capsule None devteam parents: diff changeset	5
e928e029f6eb Imported from capsule None devteam parents: diff changeset	6 usage: %prog primary_file features_file out_file direction
e928e029f6eb Imported from capsule None devteam parents: diff changeset	7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
e928e029f6eb Imported from capsule None devteam parents: diff changeset	8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
e928e029f6eb Imported from capsule None devteam parents: diff changeset	9 -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
e928e029f6eb Imported from capsule None devteam parents: diff changeset	10 -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
e928e029f6eb Imported from capsule None devteam parents: diff changeset	11 """
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	12 from __future__ import print_function
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	13
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	14 import fileinput
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	15 import sys
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	16
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	17 from bx.cookbook import doc_optparse
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	18 from bx.intervals.io import Comment, GenomicInterval, Header, NiceReaderWrapper
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	19 from bx.intervals.operations import quicksect
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	20 from bx.tabular.io import ParseError
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	21 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	22
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	23 from utils.gff_util import convert_bed_coords_to_gff, GFFIntervalToBEDReaderWrapper
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	24
e928e029f6eb Imported from capsule None devteam parents: diff changeset	25 assert sys.version_info[:2] >= ( 2, 4 )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	26
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	27
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	28 def get_closest_feature(node, direction, threshold_up, threshold_down, report_func_up, report_func_down):
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	29 # direction=1 for +ve strand upstream and -ve strand downstream cases; and it is 0 for +ve strand downstream and -ve strand upstream cases
94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	30 # threhold_Up is equal to the interval start for +ve strand, and interval end for -ve strand
94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	31 # threhold_down is equal to the interval end for +ve strand, and interval start for -ve strand
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	32 if direction == 1:
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	33 if node.maxend <= threshold_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	34 if node.end == node.maxend:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	35 report_func_up(node)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	36 elif node.right and node.left:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	37 if node.right.maxend == node.maxend:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	38 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	39 elif node.left.maxend == node.maxend:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	40 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	41 elif node.right and node.right.maxend == node.maxend:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	42 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	43 elif node.left and node.left.maxend == node.maxend:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	44 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	45 elif node.minend <= threshold_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	46 if node.end <= threshold_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	47 report_func_up(node)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	48 if node.left and node.right:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	49 if node.right.minend <= threshold_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	50 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	51 if node.left.minend <= threshold_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	52 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	53 elif node.left:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	54 if node.left.minend <= threshold_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	55 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	56 elif node.right:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	57 if node.right.minend <= threshold_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	58 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	59 elif direction == 0:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	60 if node.start > threshold_down:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	61 report_func_down(node)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	62 if node.left:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	63 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	64 else:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	65 if node.right:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	66 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	67
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	68
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	69 def proximal_region_finder(readers, region, comments=True):
e928e029f6eb Imported from capsule None devteam parents: diff changeset	70 """
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	71 Returns an iterator that yields elements of the form [ <original_interval>, <closest_feature> ].
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	72 Intervals are GenomicInterval objects.
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	73 """
e928e029f6eb Imported from capsule None devteam parents: diff changeset	74 primary = readers[0]
e928e029f6eb Imported from capsule None devteam parents: diff changeset	75 features = readers[1]
e928e029f6eb Imported from capsule None devteam parents: diff changeset	76 either = False
e928e029f6eb Imported from capsule None devteam parents: diff changeset	77 if region == 'Upstream':
e928e029f6eb Imported from capsule None devteam parents: diff changeset	78 up, down = True, False
e928e029f6eb Imported from capsule None devteam parents: diff changeset	79 elif region == 'Downstream':
e928e029f6eb Imported from capsule None devteam parents: diff changeset	80 up, down = False, True
e928e029f6eb Imported from capsule None devteam parents: diff changeset	81 else:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	82 up, down = True, True
e928e029f6eb Imported from capsule None devteam parents: diff changeset	83 if region == 'Either':
e928e029f6eb Imported from capsule None devteam parents: diff changeset	84 either = True
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	85
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	86 # Read features into memory:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	87 rightTree = quicksect.IntervalTree()
e928e029f6eb Imported from capsule None devteam parents: diff changeset	88 for item in features:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	89 if type( item ) is GenomicInterval:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	90 rightTree.insert( item, features.linenum, item )
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	91
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	92 for interval in primary:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	93 if type( interval ) is Header:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	94 yield interval
e928e029f6eb Imported from capsule None devteam parents: diff changeset	95 if type( interval ) is Comment and comments:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	96 yield interval
e928e029f6eb Imported from capsule None devteam parents: diff changeset	97 elif type( interval ) == GenomicInterval:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	98 chrom = interval.chrom
e928e029f6eb Imported from capsule None devteam parents: diff changeset	99 start = int(interval.start)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	100 end = int(interval.end)
e928e029f6eb Imported from capsule None devteam parents: diff changeset	101 strand = interval.strand
e928e029f6eb Imported from capsule None devteam parents: diff changeset	102 if chrom not in rightTree.chroms:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	103 continue
e928e029f6eb Imported from capsule None devteam parents: diff changeset	104 else:
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	105 root = rightTree.chroms[chrom] # root node for the chrom tree
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	106 result_up = []
e928e029f6eb Imported from capsule None devteam parents: diff changeset	107 result_down = []
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	108 if (strand == '+' and up) or (strand == '-' and down):
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	109 # upstream +ve strand and downstream -ve strand cases
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	110 get_closest_feature(root, 1, start, None, lambda node: result_up.append( node ), None)
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	111
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	112 if (strand == '+' and down) or (strand == '-' and up):
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	113 # downstream +ve strand and upstream -ve strand case
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	114 get_closest_feature(root, 0, None, end - 1, None, lambda node: result_down.append( node ))
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	115
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	116 if result_up:
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	117 if len(result_up) > 1: # The results_up list has a list of intervals upstream to the given interval.
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	118 ends = []
e928e029f6eb Imported from capsule None devteam parents: diff changeset	119 for n in result_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	120 ends.append(n.end)
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	121 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
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	122 else:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	123 res_ind = 0
e928e029f6eb Imported from capsule None devteam parents: diff changeset	124 if not(either):
e928e029f6eb Imported from capsule None devteam parents: diff changeset	125 yield [ interval, result_up[res_ind].other ]
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	126
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	127 if result_down:
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	128 if not(either):
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	129 # The last element of result_down will be the closest element to the given interval
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	130 yield [ interval, result_down[-1].other ]
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	131
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	132 if either and (result_up or result_down):
e928e029f6eb Imported from capsule None devteam parents: diff changeset	133 iter_val = []
e928e029f6eb Imported from capsule None devteam parents: diff changeset	134 if result_up and result_down:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	135 if abs(start - int(result_up[res_ind].end)) <= abs(end - int(result_down[-1].start)):
e928e029f6eb Imported from capsule None devteam parents: diff changeset	136 iter_val = [ interval, result_up[res_ind].other ]
e928e029f6eb Imported from capsule None devteam parents: diff changeset	137 else:
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	138 # The last element of result_down will be the closest element to the given interval
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	139 iter_val = [ interval, result_down[-1].other ]
e928e029f6eb Imported from capsule None devteam parents: diff changeset	140 elif result_up:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	141 iter_val = [ interval, result_up[res_ind].other ]
e928e029f6eb Imported from capsule None devteam parents: diff changeset	142 elif result_down:
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	143 # The last element of result_down will be the closest element to the given interval
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	144 iter_val = [ interval, result_down[-1].other ]
e928e029f6eb Imported from capsule None devteam parents: diff changeset	145 yield iter_val
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	146
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	147
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	148 def main():
e928e029f6eb Imported from capsule None devteam parents: diff changeset	149 options, args = doc_optparse.parse( __doc__ )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	150 try:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	151 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	152 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	153 in1_gff_format = bool( options.gff1 )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	154 in2_gff_format = bool( options.gff2 )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	155 in_fname, in2_fname, out_fname, direction = args
e928e029f6eb Imported from capsule None devteam parents: diff changeset	156 except:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	157 doc_optparse.exception()
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	158
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	159 # Set readers to handle either GFF or default format.
e928e029f6eb Imported from capsule None devteam parents: diff changeset	160 if in1_gff_format:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	161 in1_reader_wrapper = GFFIntervalToBEDReaderWrapper
e928e029f6eb Imported from capsule None devteam parents: diff changeset	162 else:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	163 in1_reader_wrapper = NiceReaderWrapper
e928e029f6eb Imported from capsule None devteam parents: diff changeset	164 if in2_gff_format:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	165 in2_reader_wrapper = GFFIntervalToBEDReaderWrapper
e928e029f6eb Imported from capsule None devteam parents: diff changeset	166 else:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	167 in2_reader_wrapper = NiceReaderWrapper
e928e029f6eb Imported from capsule None devteam parents: diff changeset	168
e928e029f6eb Imported from capsule None devteam parents: diff changeset	169 g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ),
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	170 chrom_col=chr_col_1,
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	171 start_col=start_col_1,
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	172 end_col=end_col_1,
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	173 strand_col=strand_col_1,
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	174 fix_strand=True )
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	175 g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	176 chrom_col=chr_col_2,
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	177 start_col=start_col_2,
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	178 end_col=end_col_2,
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	179 strand_col=strand_col_2,
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	180 fix_strand=True )
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	181
e928e029f6eb Imported from capsule None devteam parents: diff changeset	182 # Find flanking features.
e928e029f6eb Imported from capsule None devteam parents: diff changeset	183 out_file = open( out_fname, "w" )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	184 try:
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	185 for result in proximal_region_finder([g1, g2], direction):
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	186 if type( result ) is list:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	187 line, closest_feature = result
e928e029f6eb Imported from capsule None devteam parents: diff changeset	188 # Need to join outputs differently depending on file types.
e928e029f6eb Imported from capsule None devteam parents: diff changeset	189 if in1_gff_format:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	190 # Output is GFF with added attribute 'closest feature.'
e928e029f6eb Imported from capsule None devteam parents: diff changeset	191
e928e029f6eb Imported from capsule None devteam parents: diff changeset	192 # Invervals are in BED coordinates; need to convert to GFF.
e928e029f6eb Imported from capsule None devteam parents: diff changeset	193 line = convert_bed_coords_to_gff( line )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	194 closest_feature = convert_bed_coords_to_gff( closest_feature )
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	195
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	196 # Replace double quotes with single quotes in closest feature's attributes.
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	197 out_file.write( "%s closest_feature \"%s\" \n" %
850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	198 ( "\t".join( line.fields ),
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	199 "\t".join( closest_feature.fields ).replace( "\"", "\\\"" )
1 850c05b9af00 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	200 ) )
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	201 else:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	202 # Output is BED + closest feature fields.
e928e029f6eb Imported from capsule None devteam parents: diff changeset	203 output_line_fields = []
e928e029f6eb Imported from capsule None devteam parents: diff changeset	204 output_line_fields.extend( line.fields )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	205 output_line_fields.extend( closest_feature.fields )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	206 out_file.write( "%s\n" % ( "\t".join( output_line_fields ) ) )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	207 else:
e928e029f6eb Imported from capsule None devteam parents: diff changeset	208 out_file.write( "%s\n" % result )
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	209 except ParseError as exc:
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	210 fail( "Invalid file format: %s" % str( exc ) )
e928e029f6eb Imported from capsule None devteam parents: diff changeset	211
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	212 print("Direction: %s" % (direction))
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	213 if g1.skipped > 0:
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	214 print(skipped( g1, filedesc=" of 1st dataset" ))
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	215 if g2.skipped > 0:
3 94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	216 print(skipped( g2, filedesc=" of 2nd dataset" ))
94248d5b9b8b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 devteam parents: 1 diff changeset	217
0 e928e029f6eb Imported from capsule None devteam parents: diff changeset	218
e928e029f6eb Imported from capsule None devteam parents: diff changeset	219 if __name__ == "__main__":
e928e029f6eb Imported from capsule None devteam parents: diff changeset	220 main()

Mercurial > repos > devteam > flanking_features

annotate flanking_features.py @ 3:94248d5b9b8b draft default tip