# HG changeset patch
# User devteam
# Date 1396363870 14400
# Node ID a72f0decd7b3a54d54ad5b48a2368f0d361ac74d
Imported from capsule None
diff -r 000000000000 -r a72f0decd7b3 get_flanks.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/get_flanks.py Tue Apr 01 10:51:10 2014 -0400
@@ -0,0 +1,189 @@
+#!/usr/bin/env python
+#Done by: Guru
+
+"""
+Get Flanking regions.
+
+usage: %prog input out_file size direction region
+ -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
+ -o, --off=N: Offset
+"""
+
+import sys, re, os
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+def stop_err( msg ):
+ sys.stderr.write( msg )
+ sys.exit()
+
+def main():
+ try:
+ if int( sys.argv[3] ) < 0:
+ raise Exception
+ except:
+ stop_err( "Length of flanking region(s) must be a non-negative integer." )
+
+ # Parsing Command Line here
+ options, args = doc_optparse.parse( __doc__ )
+ try:
+ chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
+ inp_file, out_file, size, direction, region = args
+ if strand_col_1 <= 0:
+ strand = "+" #if strand is not defined, default it to +
+ except:
+ stop_err( "Metadata issue, correct the metadata attributes by clicking on the pencil icon in the history item." )
+ try:
+ offset = int(options.off)
+ size = int(size)
+ except:
+ stop_err( "Invalid offset or length entered. Try again by entering valid integer values." )
+
+ fo = open(out_file,'w')
+
+ skipped_lines = 0
+ first_invalid_line = 0
+ invalid_line = None
+ elems = []
+ j=0
+ for i, line in enumerate( file( inp_file ) ):
+ line = line.strip()
+ if line and (not line.startswith( '#' )) and line != '':
+ j+=1
+ try:
+ elems = line.split('\t')
+ #if the start and/or end columns are not numbers, skip that line.
+ assert int(elems[start_col_1])
+ assert int(elems[end_col_1])
+ if strand_col_1 != -1:
+ strand = elems[strand_col_1]
+ #if the stand value is not + or -, skip that line.
+ assert strand in ['+', '-']
+ if direction == 'Upstream':
+ if strand == '+':
+ if region == 'end':
+ elems[end_col_1] = str(int(elems[end_col_1]) + offset)
+ elems[start_col_1] = str( int(elems[end_col_1]) - size )
+ else:
+ elems[end_col_1] = str(int(elems[start_col_1]) + offset)
+ elems[start_col_1] = str( int(elems[end_col_1]) - size )
+ elif strand == '-':
+ if region == 'end':
+ elems[start_col_1] = str(int(elems[start_col_1]) - offset)
+ elems[end_col_1] = str(int(elems[start_col_1]) + size)
+ else:
+ elems[start_col_1] = str(int(elems[end_col_1]) - offset)
+ elems[end_col_1] = str(int(elems[start_col_1]) + size)
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+
+ elif direction == 'Downstream':
+ if strand == '-':
+ if region == 'start':
+ elems[end_col_1] = str(int(elems[end_col_1]) - offset)
+ elems[start_col_1] = str( int(elems[end_col_1]) - size )
+ else:
+ elems[end_col_1] = str(int(elems[start_col_1]) - offset)
+ elems[start_col_1] = str( int(elems[end_col_1]) - size )
+ elif strand == '+':
+ if region == 'start':
+ elems[start_col_1] = str(int(elems[start_col_1]) + offset)
+ elems[end_col_1] = str(int(elems[start_col_1]) + size)
+ else:
+ elems[start_col_1] = str(int(elems[end_col_1]) + offset)
+ elems[end_col_1] = str(int(elems[start_col_1]) + size)
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+
+ elif direction == 'Both':
+ if strand == '-':
+ if region == 'start':
+ start = str(int(elems[end_col_1]) - offset)
+ end1 = str(int(start) + size)
+ end2 = str(int(start) - size)
+ elems[start_col_1]=start
+ elems[end_col_1]=end1
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elems[start_col_1]=end2
+ elems[end_col_1]=start
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elif region == 'end':
+ start = str(int(elems[start_col_1]) - offset)
+ end1 = str(int(start) + size)
+ end2 = str(int(start) - size)
+ elems[start_col_1]=start
+ elems[end_col_1]=end1
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elems[start_col_1]=end2
+ elems[end_col_1]=start
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ else:
+ start1 = str(int(elems[end_col_1]) - offset)
+ end1 = str(int(start1) + size)
+ start2 = str(int(elems[start_col_1]) - offset)
+ end2 = str(int(start2) - size)
+ elems[start_col_1]=start1
+ elems[end_col_1]=end1
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elems[start_col_1]=end2
+ elems[end_col_1]=start2
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elif strand == '+':
+ if region == 'start':
+ start = str(int(elems[start_col_1]) + offset)
+ end1 = str(int(start) - size)
+ end2 = str(int(start) + size)
+ elems[start_col_1]=end1
+ elems[end_col_1]=start
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elems[start_col_1]=start
+ elems[end_col_1]=end2
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elif region == 'end':
+ start = str(int(elems[end_col_1]) + offset)
+ end1 = str(int(start) - size)
+ end2 = str(int(start) + size)
+ elems[start_col_1]=end1
+ elems[end_col_1]=start
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elems[start_col_1]=start
+ elems[end_col_1]=end2
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ else:
+ start1 = str(int(elems[start_col_1]) + offset)
+ end1 = str(int(start1) - size)
+ start2 = str(int(elems[end_col_1]) + offset)
+ end2 = str(int(start2) + size)
+ elems[start_col_1]=end1
+ elems[end_col_1]=start1
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ elems[start_col_1]=start2
+ elems[end_col_1]=end2
+ assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
+ fo.write( "%s\n" % '\t'.join( elems ) )
+ except:
+ skipped_lines += 1
+ if not invalid_line:
+ first_invalid_line = i + 1
+ invalid_line = line
+ fo.close()
+
+ if skipped_lines == j:
+ stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
+ if skipped_lines > 0:
+ print 'Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
+ print 'Location: %s, Region: %s, Flank-length: %d, Offset: %d ' %( direction, region, size, offset )
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r a72f0decd7b3 get_flanks.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/get_flanks.xml Tue Apr 01 10:51:10 2014 -0400
@@ -0,0 +1,82 @@
+
+ returns flanking region/s for every gene
+
+ bx-python
+ galaxy-ops
+
+ get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
+
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+
+This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
+
+**Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".
+
+-----
+
+
+**Example 1**
+
+- For the following dataset::
+
+ chr22 1000 7000 NM_174568 0 +
+
+- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**::
+
+ chr22 500 800 NM_174568 0 +
+
+.. image:: ${static_path}/operation_icons/flanks_ex1.gif
+
+**Example 2**
+
+- For the following dataset::
+
+ chr22 1000 7000 NM_028946 0 -
+
+- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::
+
+ chr22 500 800 NM_028946 0 -
+
+.. image:: ${static_path}/operation_icons/flanks_ex2.gif
+
+
+
+
+
diff -r 000000000000 -r a72f0decd7b3 test-data/flanks_inp.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flanks_inp.bed Tue Apr 01 10:51:10 2014 -0400
@@ -0,0 +1,1393 @@
+chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 +
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+chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 +
+chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 +
+chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 +
+chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 +
+chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 +
+chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 +
+chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 +
+chr7 115485764 115485980 CCDS5764.1_cds_3_0_chr7_115485765_f 0 +
+chr7 115486322 115486481 CCDS5764.1_cds_4_0_chr7_115486323_f 0 +
+chr7 115491298 115491487 CCDS5764.1_cds_5_0_chr7_115491299_f 0 +
+chr7 115733786 115733936 CCDS5766.1_cds_0_0_chr7_115733787_f 0 +
+chr7 115734264 115734452 CCDS5766.1_cds_1_0_chr7_115734265_f 0 +
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+chr7 116837536 116837787 CCDS5773.1_cds_16_0_chr7_116837537_f 0 +
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+chr7 116844523 116844674 CCDS5773.1_cds_18_0_chr7_116844524_f 0 +
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+chr7 116861526 116861775 CCDS5773.1_cds_21_0_chr7_116861527_f 0 +
+chr7 116876442 116876598 CCDS5773.1_cds_22_0_chr7_116876443_f 0 +
+chr7 116886846 116886936 CCDS5773.1_cds_23_0_chr7_116886847_f 0 +
+chr7 116898692 116898865 CCDS5773.1_cds_24_0_chr7_116898693_f 0 +
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+chr7 116900912 116901113 CCDS5773.1_cds_26_0_chr7_116900913_f 0 +
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
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+chr5 131425903 131425993 CCDS4149.1_cds_2_0_chr5_131425904_f 0 +
+chr5 131426117 131426159 CCDS4149.1_cds_3_0_chr5_131426118_f 0 +
+chr5 131426260 131426383 CCDS4149.1_cds_4_0_chr5_131426261_f 0 +
+chr5 131437415 131437574 CCDS4150.1_cds_0_0_chr5_131437416_f 0 +
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+chr5 131439336 131439444 CCDS4150.1_cds_3_0_chr5_131439337_f 0 +
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
+chr5 131626200 131626352 CCDS4152.1_cds_1_0_chr5_131626201_f 0 +
+chr5 131630055 131630137 CCDS4152.1_cds_2_0_chr5_131630056_f 0 +
+chr5 131634506 131634685 CCDS4152.1_cds_3_0_chr5_131634507_f 0 +
+chr5 131634894 131635058 CCDS4152.1_cds_4_0_chr5_131634895_f 0 +
+chr5 131635382 131635500 CCDS4152.1_cds_5_0_chr5_131635383_f 0 +
+chr5 131635616 131635821 CCDS4152.1_cds_6_0_chr5_131635617_f 0 +
+chr5 131658208 131658601 CCDS4153.1_cds_0_0_chr5_131658209_f 0 +
+chr5 131675752 131675856 CCDS4153.1_cds_1_0_chr5_131675753_f 0 +
+chr5 131677205 131677360 CCDS4153.1_cds_2_0_chr5_131677206_f 0 +
+chr5 131685775 131685947 CCDS4153.1_cds_3_0_chr5_131685776_f 0 +
+chr5 131690868 131690995 CCDS4153.1_cds_4_0_chr5_131690869_f 0 +
+chr5 131695347 131695442 CCDS4153.1_cds_5_0_chr5_131695348_f 0 +
+chr5 131698309 131698524 CCDS4153.1_cds_6_0_chr5_131698310_f 0 +
+chr5 131699409 131699592 CCDS4153.1_cds_7_0_chr5_131699410_f 0 +
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diff -r 000000000000 -r a72f0decd7b3 test-data/flanks_out1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flanks_out1.bed Tue Apr 01 10:51:10 2014 -0400
@@ -0,0 +1,2786 @@
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diff -r 000000000000 -r a72f0decd7b3 test-data/flanks_out2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flanks_out2.bed Tue Apr 01 10:51:10 2014 -0400
@@ -0,0 +1,1393 @@
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diff -r 000000000000 -r a72f0decd7b3 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Apr 01 10:51:10 2014 -0400
@@ -0,0 +1,9 @@
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