Mercurial > repos > devteam > windowsplitter
changeset 0:4815516900d4
Imported from capsule None
| author | devteam |
|---|---|
| date | Tue, 01 Apr 2014 09:12:19 -0400 |
| parents | |
| children | 477a0cfe6e6c |
| files | test-data/4.bed test-data/4_windows.bed windowSplitter.py windowSplitter.xml |
| diffstat | 4 files changed, 613 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4.bed Tue Apr 01 09:12:19 2014 -0400 @@ -0,0 +1,1 @@ +chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/windowSplitter.py Tue Apr 01 09:12:19 2014 -0400 @@ -0,0 +1,84 @@ +#!/usr/bin/env python + +""" +Split into windows. + +usage: %prog input size out_file + -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file +""" + +import sys + +from galaxy import eggs +import pkg_resources +pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse +from galaxy.tools.util.galaxyops import * + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + + +def main(): + # 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, winsize, out_file, makesliding, offset = args + winsize = int(winsize) + offset = int(offset) + makesliding = int(makesliding) + except: + stop_err( "Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset." ) + + fo = open(out_file,'w') + + skipped_lines = 0 + first_invalid_line = 0 + invalid_line = None + if offset == 0: + makesliding = 0 + + for i, line in enumerate( file( inp_file ) ): + line = line.strip() + if line and line[0:1] != "#": + try: + elems = line.split('\t') + start = int(elems[start_col_1]) + end = int(elems[end_col_1]) + if makesliding == 0: + numwin = (end - start)/winsize + else: + numwin = (end - start)/offset + if numwin > 0: + for win in range(numwin): + elems_1 = elems + elems_1[start_col_1] = str(start) + elems_1[end_col_1] = str(start + winsize) + fo.write( "%s\n" % '\t'.join( elems_1 ) ) + if makesliding == 0: + start = start + winsize + else: + start = start + offset + if start+winsize > end: + break + except: + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + + fo.close() + + if makesliding == 1: + print 'Window size=%d, Sliding=Yes, Offset=%d' % ( winsize, offset ) + else: + print 'Window size=%d, Sliding=No' % (winsize) + if skipped_lines > 0: + print 'Skipped %d invalid lines starting with #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/windowSplitter.xml Tue Apr 01 09:12:19 2014 -0400 @@ -0,0 +1,104 @@ +<tool id="winSplitter" name="Make windows" version="0.0.1"> + <description></description> + <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command> + <inputs> + <!--<param label="Genome" name="dbkey" type="genomebuild"/>--> + <param format="interval" name="input" type="data" label="Select data"/> + <param name="size" size="10" type="integer" value="500" label="Window size"/> + <conditional name="wintype"> + <param name="choice" type="select" label="Make sliding windows?"> + <option value="0" selected="true">No</option> + <option value="1">Yes</option> + </param> + <when value="0"> + <param name="offset" type="hidden" value="0" /> + </when> + <when value="1"> + <param name="offset" size="10" type="integer" value="10" label="Offset size"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="interval" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="input" value="4.bed"/> + <param name="size" value="5000"/> + <param name="choice" value="1"/> + <param name="offset" value="4000"/> + <output name="out_file1" file="4_windows.bed"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What it does** + +This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type. + +----- + +.. class:: warningmark + +**Note** + +The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output. + +----- + +.. class:: infomark + +**About formats** + +**BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones: + +The first three BED fields (required) are:: + + 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). + 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) + 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). + +The additional BED fields (optional) are:: + + 4. name - The name of the BED line. + 5. score - A score between 0 and 1000. + 6. strand - Defines the strand - either '+' or '-'. + 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. + 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. + 9. reserved - This should always be set to zero. + 10. blockCount - The number of blocks (exons) in the BED line. + 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. + 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount. + 13. expCount - The number of experiments. + 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount. + 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount. + +----- + +**Example** + +- For the following dataset:: + + chr22 1000 4700 NM_174568 0 + + +- running this tool with **Window size as 1000**, will return:: + + chr22 1000 2000 NM_174568 0 + + chr22 2000 3000 NM_174568 0 + + chr22 3000 4000 NM_174568 0 + + +- running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return:: + + chr22 1000 2000 NM_174568 0 + + chr22 1500 2500 NM_174568 0 + + chr22 2000 3000 NM_174568 0 + + chr22 2500 3500 NM_174568 0 + + chr22 3000 4000 NM_174568 0 + + chr22 3500 4500 NM_174568 0 + + + </help> + + +</tool>