Mercurial > repos > devteam > get_flanks
changeset 0:a72f0decd7b3
Imported from capsule None
| author | devteam |
|---|---|
| date | Tue, 01 Apr 2014 10:51:10 -0400 |
| parents | |
| children | c3b1781c6fd1 |
| files | get_flanks.py get_flanks.xml test-data/flanks_inp.bed test-data/flanks_out1.bed test-data/flanks_out2.bed tool_dependencies.xml |
| diffstat | 6 files changed, 5852 insertions(+), 0 deletions(-) [+] |
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--- /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()
--- /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 @@ +<tool id="get_flanks1" name="Get flanks" version="0.0.1"> + <description>returns flanking region/s for every gene</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">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command> + <inputs> + <param format="interval" name="input" type="data" label="Select data"/> + <param name="region" type="select" label="Region"> + <option value="whole" selected="true">Whole feature</option> + <option value="start">Around Start</option> + <option value="end">Around End</option> + </param> + <param name="direction" type="select" label="Location of the flanking region/s"> + <option value="Upstream">Upstream</option> + <option value="Downstream">Downstream</option> + <option value="Both">Both</option> + </param> + <param name="offset" size="10" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/> + <param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/> + + + </inputs> + <outputs> + <data format="interval" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="input" value="flanks_inp.bed"/> + <param name="offset" value="-500"/> + <param name="size" value="1000"/> + <param name="direction" value="Both"/> + <param name="region" value="whole"/> + <output name="out_file1" file="flanks_out1.bed"/> + </test> + <test> + <param name="input" value="flanks_inp.bed"/> + <param name="offset" value="200"/> + <param name="size" value="1000"/> + <param name="direction" value="Downstream"/> + <param name="region" value="start" /> + <output name="out_file1" file="flanks_out2.bed"/> + </test> + </tests> + <help> + +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 + +</help> + + +</tool>
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--- /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 @@ +<?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>