GalaxyChangeset 1334:0cf33730c91c
- Timestamp:
- 05/28/08 15:26:42 (7 months ago)
- Files:
-
- test-data/2.lav (added)
- test-data/lav_to_bed_out2.bed (added)
- test-data/scatterplot_in1.tabular (modified) (1 diff)
- tools/filters/BedLike2Text.pl (deleted)
- tools/filters/BedLike2Text.xml (deleted)
- tools/filters/Interval2BedLike.pl (deleted)
- tools/filters/Interval2BedLike.xml (deleted)
- tools/filters/Text2BedLike.pl (deleted)
- tools/filters/Text2BedLike.xml (deleted)
- tools/filters/aggTrack.pl (deleted)
- tools/filters/aggTrack.xml (deleted)
- tools/filters/lav_to_bed.py (modified) (2 diffs)
- tools/filters/lav_to_bed.xml (modified) (5 diffs)
- tools/filters/lav_to_bed_code.py (modified) (1 diff)
- tools/filters/random_lines.py (deleted)
- tools/filters/random_lines.xml (deleted)
- tools/filters/srg2wig.pl (deleted)
- tools/filters/srg2wig.xml (deleted)
- universe_wsgi.ini.sample (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
- Modified
- Copied
- Moved
test-data/scatterplot_in1.tabular
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r1213 r1334 1 1 #!/usr/bin/env python 2 2 #Reads a LAV file and writes two BED files. 3 4 3 import sys 5 4 from galaxy import eggs … … 10 9 assert sys.version_info[:2] >= ( 2, 4 ) 11 10 11 def stop_err( msg ): 12 sys.stderr.write( msg ) 13 sys.exit() 14 12 15 def main(): 13 14 16 try: 15 17 lav_file = open(sys.argv[1],'r') 16 18 bed_file1 = open(sys.argv[2],'w') 17 19 bed_file2 = open(sys.argv[3],'w') 18 except: 19 print >>sys.stderr,"Error with provided arguments" 20 print >>sys.stderr,"Usage: python %s input_lav output_bed1 output_bed2" % sys.argv[0] 21 sys.exit(0) 20 except Exception, e: 21 stop_err( str( e ) ) 22 22 23 lavsRead = bedsWritten = 0 23 lavsRead = 0 24 bedsWritten = 0 24 25 species = {} 25 for lavBlock in bx.align.lav.Reader(lav_file): 26 # TODO: this is really bad since everything is read into memory. Can we eliminate this tool? 27 for lavBlock in bx.align.lav.Reader( lav_file ): 26 28 lavsRead += 1 27 28 29 for c in lavBlock.components: 29 spec, chrom = bx.align.lav.src_split( c.src )30 spec, chrom = bx.align.lav.src_split( c.src ) 30 31 if bedsWritten < 1: 31 if len( species)==0:32 if len( species )==0: 32 33 species[spec]=bed_file1 33 elif len( species)==1:34 elif len( species )==1: 34 35 species[spec]=bed_file2 35 36 else: 36 37 continue #this is a pairwise alignment... 37 38 if spec in species: 38 species[spec].write( "%s\t%i\t%i\t%s\t%i\t%s\n" % (chrom,c.start,c.end,spec+"_"+str(bedsWritten),0,c.strand))39 species[spec].write( "%s\t%i\t%i\t%s_%s\t%i\t%s\n" % ( chrom, c.start, c.end, spec, str( bedsWritten ), 0, c.strand ) ) 39 40 bedsWritten += 1 40 41 41 42 42 43 for spec,file in species.items(): tools/filters/lav_to_bed.xml
r1129 r1334 1 1 <tool id="lav_to_bed1" name="LAV to BED"> 2 <description>Converts a LAV formated file to BED format</description> 3 <command interpreter="python">lav_to_bed.py $lav_file $bed_file1 $bed_file2</command> 4 2 <description>Converts a LAV formated file to BED format</description> 3 <command interpreter="python">lav_to_bed.py $lav_file $bed_file1 $bed_file2</command> 5 4 <inputs> 6 <page> 7 <param name="lav_file" type="data" format="lav" label="LAV File" optional="False"/> 8 </page> 5 <param name="lav_file" type="data" format="lav" label="LAV File" optional="False"/> 9 6 </inputs> 10 7 <outputs> … … 12 9 <data name="bed_file2" format="bed"/> 13 10 </outputs> 14 <help> 11 <tests> 12 <!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated --> 13 <test> 14 <param name="lav_file" value="2.lav" ftype="lav" /> 15 <output name="bed_file2" file="lav_to_bed_out2.bed" /> 16 </test> 17 </tests> 18 <help> 15 19 16 20 **Syntax** … … 18 22 This tool converts a LAV formated file to the BED format. 19 23 20 - **LAV format** LAV is an alignment format developed by Webb Miller's group . It is the primary output format for BLASTZ.24 - **LAV format** LAV is an alignment format developed by Webb Miller's group at Penn State University. It is the primary output format for BLASTZ. 21 25 22 - **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and twelve additional optional ones:: 23 24 The first three BED fields (required) are: 25 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). 26 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) 27 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). 28 29 Additional (optional) fields are: 30 4. name - The name of the BED line. 31 5. score - A score between 0 and 1000. 32 6. strand - Defines the strand - either '+' or '-'. 26 - **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. 33 27 34 28 ----- … … 41 35 s { 42 36 "/depot/data2/galaxy/hg16/seq/chr19.nib" 1 63811651 0 1 43 "/depot/data2/galaxy/mm5/seq/chr11.nib -" 1 121648857 0 137 "/depot/data2/galaxy/mm5/seq/chr11.nib" 1 121648857 0 1 44 38 } 45 39 h { … … 70 64 chr11 70568379 70568443 mm5_0 0 + 71 65 chr11 70573975 70574054 mm5_1 0 + 72 73 66 </help> 67 <code file="lav_to_bed_code.py"/> 74 68 </tool> tools/filters/lav_to_bed_code.py
r1012 r1334 8 8 filename_to_build[fields[1]]=fields[2].strip() 9 9 else: 10 new_stdout = new_stdout + line10 new_stdout = "%s%s" % ( new_stdout, line ) 11 11 for name,data in out_data.items(): 12 12 try: 13 data.info = new_stdout +"\n"+ stderr13 data.info = "%s\n%s" % ( new_stdout, stderr ) 14 14 data.dbkey = filename_to_build[data.file_name] 15 data.name = data.name + " ("+data.dbkey+")"15 data.name = "%s (%s)" % ( data.name, data.dbkey ) 16 16 data.flush() 17 17 except: universe_wsgi.ini.sample
r1329 r1334 185 185 jpg = galaxy.datatypes.images:Image,image/jpeg 186 186 laj = galaxy.datatypes.images:Laj 187 lav = galaxy.datatypes.sequence:Lav 187 lav = galaxy.datatypes.sequence:Lav,display_in_upload 188 188 maf = galaxy.datatypes.sequence:Maf,display_in_upload 189 189 pdf = galaxy.datatypes.images:Image,application/pdf
