changeset 0:e5490ea33640

Imported from capsule None
author devteam
date Tue, 01 Apr 2014 10:50:03 -0400
parents
children 75abda2290cc
files test-data/4.bed test-data/4_windows.bed windowSplitter.py windowSplitter.xml
diffstat 4 files changed, 613 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4.bed	Tue Apr 01 10:50:03 2014 -0400
@@ -0,0 +1,1 @@
+chr22	30128507	31828507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4_windows.bed	Tue Apr 01 10:50:03 2014 -0400
@@ -0,0 +1,424 @@
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+chr22	31744507	31749507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31748507	31753507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31752507	31757507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31756507	31761507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31760507	31765507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31764507	31769507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31768507	31773507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31772507	31777507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31776507	31781507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31780507	31785507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31784507	31789507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31788507	31793507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31792507	31797507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31796507	31801507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31800507	31805507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31804507	31809507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31808507	31813507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31812507	31817507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31816507	31821507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31820507	31825507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/windowSplitter.py	Tue Apr 01 10:50:03 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 10:50:03 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>