# HG changeset patch # User devteam # Date 1396363803 14400 # Node ID e5490ea3364013147377560c8e616305ccd1d4a6 Imported from capsule None diff -r 000000000000 -r e5490ea33640 test-data/4.bed --- /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 + diff -r 000000000000 -r e5490ea33640 test-data/4_windows.bed --- /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 @@ +chr22 30128507 30133507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30132507 30137507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30136507 30141507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30140507 30145507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30144507 30149507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30148507 30153507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30152507 30157507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30156507 30161507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30160507 30165507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30164507 30169507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30168507 30173507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30172507 30177507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30176507 30181507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30180507 30185507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30184507 30189507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30188507 30193507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30192507 30197507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30196507 30201507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30200507 30205507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30204507 30209507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30208507 30213507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30212507 30217507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30216507 30221507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30220507 30225507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30224507 30229507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30228507 30233507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30232507 30237507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30236507 30241507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30240507 30245507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30244507 30249507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30248507 30253507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30252507 30257507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30256507 30261507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30260507 30265507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30264507 30269507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30268507 30273507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30272507 30277507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30276507 30281507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30280507 30285507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30284507 30289507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30288507 30293507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30292507 30297507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30296507 30301507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30300507 30305507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30304507 30309507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30308507 30313507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30312507 30317507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30316507 30321507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30320507 30325507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30324507 30329507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30328507 30333507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30332507 30337507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30336507 30341507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30340507 30345507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30344507 30349507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30348507 30353507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30352507 30357507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30356507 30361507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30360507 30365507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30364507 30369507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30368507 30373507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30372507 30377507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30376507 30381507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30380507 30385507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30384507 30389507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30388507 30393507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30392507 30397507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30396507 30401507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30400507 30405507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30404507 30409507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30408507 30413507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30412507 30417507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30416507 30421507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30420507 30425507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30424507 30429507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30428507 30433507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30432507 30437507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30436507 30441507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30440507 30445507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30444507 30449507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30448507 30453507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30452507 30457507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30456507 30461507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30460507 30465507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30464507 30469507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30468507 30473507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30472507 30477507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30476507 30481507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30480507 30485507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30484507 30489507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30488507 30493507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30492507 30497507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30496507 30501507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30500507 30505507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30504507 30509507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30508507 30513507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30512507 30517507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30516507 30521507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30520507 30525507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30524507 30529507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30528507 30533507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30532507 30537507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30536507 30541507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30540507 30545507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30544507 30549507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30548507 30553507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30552507 30557507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30556507 30561507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30560507 30565507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30564507 30569507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30568507 30573507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30572507 30577507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30576507 30581507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30580507 30585507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30584507 30589507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30588507 30593507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30592507 30597507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30596507 30601507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30600507 30605507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30604507 30609507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30608507 30613507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30612507 30617507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30616507 30621507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30620507 30625507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30624507 30629507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30628507 30633507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30632507 30637507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30636507 30641507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30640507 30645507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30644507 30649507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30648507 30653507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30652507 30657507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30656507 30661507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30660507 30665507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30664507 30669507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30668507 30673507 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uc003bnx.1_cds_2_0_chr22_29227_f 0 + diff -r 000000000000 -r e5490ea33640 windowSplitter.py --- /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() diff -r 000000000000 -r e5490ea33640 windowSplitter.xml --- /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 @@ + + + windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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 + + + + + +