mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Added tool version directories to regVariation tools directory.
This commit is contained in:
Greg Von Kuster
+6
-6
@@ -117,13 +117,13 @@
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<tool file="visualization/build_ucsc_custom_track.xml" />
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</section>
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<section name="Regional Variation" id="regVar">
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<tool file="regVariation/windowSplitter.xml" />
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<tool file="regVariation/featureCounter.xml" />
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<tool file="regVariation/quality_filter.xml" />
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<tool file="regVariation/maf_cpg_filter.xml" />
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<tool file="regVariation/winSplitter/1.0.0/windowSplitter.xml" />
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<tool file="regVariation/featureCoverage1/1.0.0/featureCounter.xml" />
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<tool file="regVariation/qualityFilter/1.0.0/quality_filter.xml" />
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<tool file="regVariation/cpgFilter/1.0.0/maf_cpg_filter.xml" />
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<!--
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<tool file="regVariation/getIndels_2way.xml" />
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<tool file="regVariation/getIndels_3way.xml" />
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<tool file="regVariation/getIndels_2way/1.0.0/getIndels_2way.xml" />
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<tool file="regVariation/getIndels_3way/1.0.0/getIndels_3way.xml" />
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-->
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</section>
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<section name="Evolution: HyPhy" id="hyphy">
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@@ -122,12 +122,12 @@
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<tool file="visualization/build_ucsc_custom_track.xml" />
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</section>
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<section name="Regional Variation" id="regVar">
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<tool file="regVariation/windowSplitter.xml" />
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<tool file="regVariation/featureCounter.xml" />
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<tool file="regVariation/quality_filter.xml" />
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<tool file="regVariation/maf_cpg_filter.xml" />
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<tool file="regVariation/getIndels_2way.xml" />
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<tool file="regVariation/getIndels_3way.xml" />
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<tool file="regVariation/winSplitter/1.0.0/windowSplitter.xml" />
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<tool file="regVariation/featureCoverage1/1.0.0/featureCounter.xml" />
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<tool file="regVariation/qualityFilter/1.0.0/quality_filter.xml" />
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<tool file="regVariation/cpgFilter/1.0.0/maf_cpg_filter.xml" />
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<tool file="regVariation/getIndels_2way/1.0.0/getIndels_2way.xml" />
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<tool file="regVariation/getIndels_3way/1.0.0/getIndels_3way.xml" />
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</section>
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<section name="Evolution: HyPhy" id="hyphy">
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<tool file="hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.xml" />
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@@ -1,53 +0,0 @@
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#Adapted from bx/intervals/operations/coverage.py
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"""
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Determine amount of each interval in one set covered by the intervals of
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another set. Adds two columns to the first input, giving number of bases
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covered and percent coverage on the second input.
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"""
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import pkg_resources
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pkg_resources.require( "bx-python" )
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import psyco_full
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import traceback
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import fileinput
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from warnings import warn
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from bx.intervals.io import *
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from bx.intervals.operations import *
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def coverage(readers, comments=True):
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# Read all but first into bitsets and union to one
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primary = readers[0]
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intersect = readers[1:]
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bitsets = intersect[0].binned_bitsets()
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intersect = intersect[1:]
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for andset in intersect:
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bitset2 = andset.binned_bitsets()
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for chrom in bitsets:
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if chrom not in bitset2: continue
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bitsets[chrom].ior(bitset2[chrom])
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intersect = intersect[1:]
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# Read remaining intervals and give coverage
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for interval in primary:
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if type( interval ) is Header:
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yield interval
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if type( interval ) is Comment and comments:
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yield interval
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elif type( interval ) == GenomicInterval:
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chrom = interval.chrom
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start = int(interval.start)
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end = int(interval.end)
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if start > end: warn( "Interval start after end!" )
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if chrom not in bitsets:
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bases_covered = 0
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percent = 0.0
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else:
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bases_covered = bitsets[ chrom ].count_range( start, end-start )
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if (end - start) == 0: percent = 0
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else: percent = float(bases_covered) / float(end - start)
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interval.fields.append(str(bases_covered))
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interval.fields.append(str(percent))
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yield interval
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@@ -1,136 +0,0 @@
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#!/usr/bin/env python
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"""
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Calculate coverage of one query on another, and append the coverage to
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the last two columns as bases covered and percent coverage.
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usage: %prog bed_file_1 bed_file_2 out_file
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-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
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-2, --cols2=N,N,N,N: Columns for start, end, strand in second file
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"""
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import pkg_resources
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pkg_resources.require( "bx-python" )
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import sys
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import traceback
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import fileinput
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from warnings import warn
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#from bx.intervals import *
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from bx.intervals.io import *
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#from bx.intervals.operations.coverage import *
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from bx.cookbook import doc_optparse
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from featureCounter_code import *
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from galaxyops import *
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def main():
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upstream_pad = 0
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downstream_pad = 0
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options, args = doc_optparse.parse( __doc__ )
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try:
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chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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in_fname, in2_fname, out_fname = args
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except:
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doc_optparse.exception()
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g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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chrom_col=chr_col_1,
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start_col=start_col_1,
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end_col=end_col_1,
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strand_col=strand_col_1,
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fix_strand=True)
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g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
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chrom_col=chr_col_2,
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start_col=start_col_2,
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end_col=end_col_2,
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strand_col=strand_col_2,
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fix_strand=True)
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out_file = open( out_fname, "w" )
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chr_list = []
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start_list = []
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end_list = []
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for line in open(in2_fname, 'r'):
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line = line.rstrip("\r\n")
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if not(line) or line == "" or line[0:1] == '#':
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continue
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elems = line.split('\t')
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chr_list.append(elems[chr_col_2])
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start_list.append(elems[start_col_2])
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end_list.append(elems[end_col_2])
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for line1 in open(in_fname, 'r'):
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fp = 0 #number of features fully present
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fp_p = [] #% covered by fp features
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pp_l = 0 #partly present on left side of the window
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pp_l_p = [] #% covered by pp_l features
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pp_r = 0 #partly present on right side of the window
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pp_r_p = [] #% covered by pp_r features
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np = 0 #number of features present
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chr1 = line1.split('\t')[chr_col_1]
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start1 = int(line1.split('\t')[start_col_1])
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end1 = int(line1.split('\t')[end_col_1])
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if not(chr1 in chr_list):
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continue
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for i, chr2 in enumerate(chr_list):
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#chr2 = line2.split('\t')[chr_col_2]
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#start2 = int(line2.split('\t')[start_col_2])
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#end2 = int(line2.split('\t')[end_col_2])
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start2 = int(start_list[i])
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end2 = int(end_list[i])
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if chr2 == chr1:
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"""
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if end2 < start2:
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tmp = start2
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start2 = end2
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end2 = tmp
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"""
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if (start2 < start1 and end2 < start1) or (start2 >end1 and end2 >end1):
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continue
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if start2 in range(start1,end1):
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if end2 in range(start1,end1):
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fp+=1
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fp_p.append("%2.2f"%(100.0*abs(end2 - start2)/abs(end1-start1)))
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else:
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pp_r = pp_r + (1.0*abs(end1 - start2)/abs(end2-start2))
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pp_r_p.append("%2.2f"%(100.0*abs(end1 - start2)/abs(end1-start1)))
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#pp_r_p = pp_r_p + abs(end1 - start2)
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elif end2 in range(start1,end1):
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pp_l = pp_l + (1.0*abs(end2 - start1)/abs(end2 - start2))
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pp_l_p.append("%2.2f"%(100.0*abs(end2 - start1)/abs(end1-start1)))
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#pp_l_p = pp_l_p + abs(end2 - start1)
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else:
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if (start1 in range(start2,end2)) and (end1 in range(start2,end2)):
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fp = fp + (1.0*abs(end1 - start1)/abs(end2 - start2))
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fp_p.append('100.00')
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print >>out_file, "%s\t%2.2f\t%s\t%2.2f\t%s\t%2.2f\t%s" %(line1.strip(),fp,fp_p,pp_l,pp_l_p,pp_r,pp_r_p)
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#print >>out_file, "%s\t%d\t%2.2f\t%d\t%2.2f\t%d\t%2.2f" %(line1.strip(),fp,float(fp_p)/abs(end1-start1),pp_l,float(pp_l_p)/abs(end1-start1),pp_r,float(pp_r_p)/abs(end1-start1))
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"""
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fo=open("pfct","w")
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print >>fo, g1
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print >>fo, g2
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try:
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for line in mycoverage([g1,g2]):
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if type( line ) is GenomicInterval:
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print >> out_file, "\t".join( line.fields )
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else:
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print >> out_file, line
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except ParseError, exc:
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print >> sys.stderr, "Invalid file format: ", str( exc )
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if g1.skipped > 0:
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print skipped( g1, filedesc=" of 1st dataset" )
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if g2.skipped > 0:
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print skipped( g2, filedesc=" of 2nd dataset" )
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"""
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if __name__ == "__main__":
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main()
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@@ -1,127 +0,0 @@
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#!/usr/bin/env python
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"""
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Calculate coverage of one query on another, and append the coverage to
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the last two columns as bases covered and percent coverage.
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usage: %prog bed_file_1 bed_file_2 out_file
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-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
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-2, --cols2=N,N,N,N: Columns for start, end, strand in second file
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"""
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import pkg_resources
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pkg_resources.require( "bx-python" )
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import sys
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import traceback
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import fileinput
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from warnings import warn
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#from bx.intervals import *
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from bx.intervals.io import *
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#from bx.intervals.operations.coverage import *
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from bx.cookbook import doc_optparse
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from featureCounter_code import *
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from galaxyops import *
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def main():
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upstream_pad = 0
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downstream_pad = 0
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options, args = doc_optparse.parse( __doc__ )
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try:
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chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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in_fname, in2_fname, out_fname = args
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except:
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doc_optparse.exception()
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g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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chrom_col=chr_col_1,
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start_col=start_col_1,
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end_col=end_col_1,
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strand_col=strand_col_1,
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fix_strand=True)
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g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
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chrom_col=chr_col_2,
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start_col=start_col_2,
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end_col=end_col_2,
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strand_col=strand_col_2,
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fix_strand=True)
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out_file = open( out_fname, "w" )
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chr_list = []
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start_list = []
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end_list = []
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for line in open(in2_fname, 'r'):
|
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line = line.rstrip("\r\n")
|
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if not(line) or line == "" or line[0:1] == '#':
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continue
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elems = line.split('\t')
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chr_list.append(elems[chr_col_2])
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start_list.append(elems[start_col_2])
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end_list.append(elems[end_col_2])
|
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for line1 in open(in_fname, 'r'):
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fp = 0 #number of features fully present
|
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fp_p = [] #% covered by fp features
|
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pp_l = 0 #partly present on left side of the window
|
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pp_l_p = [] #% covered by pp_l features
|
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pp_r = 0 #partly present on right side of the window
|
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pp_r_p = [] #% covered by pp_r features
|
||||
np = 0 #number of features present
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chr1 = line1.split('\t')[chr_col_1]
|
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start1 = int(line1.split('\t')[start_col_1])
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end1 = int(line1.split('\t')[end_col_1])
|
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for line2 in open(in2_fname, 'r'):
|
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chr2 = line2.split('\t')[chr_col_2]
|
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start2 = int(line2.split('\t')[start_col_2])
|
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end2 = int(line2.split('\t')[end_col_2])
|
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if chr2 == chr1:
|
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if end2 < start2:
|
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tmp = start2
|
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start2 = end2
|
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end2 = tmp
|
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if start2 in range(start1,end1):
|
||||
if end2 in range(start1,end1):
|
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fp+=1
|
||||
fp_p.append(round(100.0*abs(end2 - start2)/abs(end1-start1)))
|
||||
else:
|
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pp_r+=1
|
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pp_r_p.append(round(100.0*abs(end1 - start2)/abs(end1-start1)))
|
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#pp_r_p = pp_r_p + abs(end1 - start2)
|
||||
elif end2 in range(start1,end1):
|
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pp_l+=1
|
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pp_l_p.append(round(100.0*abs(end2 - start1)/abs(end1-start1)))
|
||||
#pp_l_p = pp_l_p + abs(end2 - start1)
|
||||
else:
|
||||
if (start1 in range(start2,end2)) and (end1 in range(start2,end2)):
|
||||
fp+=1
|
||||
fp_p.append(100.0)
|
||||
|
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print >>out_file, "%s\t%d\t%s\t%d\t%s\t%d\t%s" %(line1.strip(),fp,fp_p,pp_l,pp_l_p,pp_r,pp_r_p)
|
||||
#print >>out_file, "%s\t%d\t%2.2f\t%d\t%2.2f\t%d\t%2.2f" %(line1.strip(),fp,float(fp_p)/abs(end1-start1),pp_l,float(pp_l_p)/abs(end1-start1),pp_r,float(pp_r_p)/abs(end1-start1))
|
||||
"""
|
||||
fo=open("pfct","w")
|
||||
print >>fo, g1
|
||||
print >>fo, g2
|
||||
try:
|
||||
for line in mycoverage([g1,g2]):
|
||||
if type( line ) is GenomicInterval:
|
||||
print >> out_file, "\t".join( line.fields )
|
||||
else:
|
||||
print >> out_file, line
|
||||
|
||||
except ParseError, exc:
|
||||
print >> sys.stderr, "Invalid file format: ", str( exc )
|
||||
|
||||
if g1.skipped > 0:
|
||||
print skipped( g1, filedesc=" of 1st dataset" )
|
||||
|
||||
if g2.skipped > 0:
|
||||
print skipped( g2, filedesc=" of 2nd dataset" )
|
||||
|
||||
"""
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
@@ -1,134 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
"""
|
||||
Calculate coverage of one query on another, and append the coverage to
|
||||
the last two columns as bases covered and percent coverage.
|
||||
|
||||
usage: %prog bed_file_1 bed_file_2 out_file
|
||||
-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
|
||||
-2, --cols2=N,N,N,N: Columns for start, end, strand in second file
|
||||
"""
|
||||
|
||||
import pkg_resources
|
||||
pkg_resources.require( "bx-python" )
|
||||
|
||||
import sys
|
||||
import traceback
|
||||
import fileinput
|
||||
from warnings import warn
|
||||
|
||||
#from bx.intervals import *
|
||||
from bx.intervals.io import *
|
||||
#from bx.intervals.operations.coverage import *
|
||||
from bx.cookbook import doc_optparse
|
||||
from featureCounter_code import *
|
||||
|
||||
from galaxyops import *
|
||||
|
||||
def main():
|
||||
|
||||
upstream_pad = 0
|
||||
downstream_pad = 0
|
||||
|
||||
options, args = doc_optparse.parse( __doc__ )
|
||||
try:
|
||||
chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
|
||||
chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
|
||||
in_fname, in2_fname, out_fname = args
|
||||
except:
|
||||
doc_optparse.exception()
|
||||
|
||||
g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
|
||||
chrom_col=chr_col_1,
|
||||
start_col=start_col_1,
|
||||
end_col=end_col_1,
|
||||
strand_col=strand_col_1,
|
||||
fix_strand=True)
|
||||
g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
|
||||
chrom_col=chr_col_2,
|
||||
start_col=start_col_2,
|
||||
end_col=end_col_2,
|
||||
strand_col=strand_col_2,
|
||||
fix_strand=True)
|
||||
out_file = open( out_fname, "w" )
|
||||
|
||||
chr_list = []
|
||||
start_list = []
|
||||
end_list = []
|
||||
for line in open(in2_fname, 'r'):
|
||||
line = line.rstrip("\r\n")
|
||||
if not(line) or line == "" or line[0:1] == '#':
|
||||
continue
|
||||
elems = line.split('\t')
|
||||
chr_list.append(elems[chr_col_2])
|
||||
start_list.append(elems[start_col_2])
|
||||
end_list.append(elems[end_col_2])
|
||||
|
||||
for line1 in open(in_fname, 'r'):
|
||||
fp = 0 #number of features fully present
|
||||
fp_p = [] #% covered by fp features
|
||||
pp_l = 0 #partly present on left side of the window
|
||||
pp_l_p = [] #% covered by pp_l features
|
||||
pp_r = 0 #partly present on right side of the window
|
||||
pp_r_p = [] #% covered by pp_r features
|
||||
np = 0 #number of features present
|
||||
chr1 = line1.split('\t')[chr_col_1]
|
||||
start1 = int(line1.split('\t')[start_col_1])
|
||||
end1 = int(line1.split('\t')[end_col_1])
|
||||
if not(chr1 in chr_list):
|
||||
continue
|
||||
for i, chr2 in enumerate(chr_list):
|
||||
#chr2 = line2.split('\t')[chr_col_2]
|
||||
#start2 = int(line2.split('\t')[start_col_2])
|
||||
#end2 = int(line2.split('\t')[end_col_2])
|
||||
start2 = int(start_list[i])
|
||||
end2 = int(end_list[i])
|
||||
if chr2 == chr1:
|
||||
"""
|
||||
if end2 < start2:
|
||||
tmp = start2
|
||||
start2 = end2
|
||||
end2 = tmp
|
||||
"""
|
||||
if start2 in range(start1,end1):
|
||||
if end2 in range(start1,end1):
|
||||
fp+=1
|
||||
fp_p.append("%2.2f"%(100.0*abs(end2 - start2)/abs(end1-start1)))
|
||||
else:
|
||||
pp_r+=1
|
||||
pp_r_p.append("%2.2f"%(100.0*abs(end1 - start2)/abs(end1-start1)))
|
||||
#pp_r_p = pp_r_p + abs(end1 - start2)
|
||||
elif end2 in range(start1,end1):
|
||||
pp_l+=1
|
||||
pp_l_p.append("%2.2f"%(100.0*abs(end2 - start1)/abs(end1-start1)))
|
||||
#pp_l_p = pp_l_p + abs(end2 - start1)
|
||||
else:
|
||||
if (start1 in range(start2,end2)) and (end1 in range(start2,end2)):
|
||||
fp+=1
|
||||
fp_p.append(100.00)
|
||||
|
||||
print >>out_file, "%s\t%d\t%s\t%d\t%s\t%d\t%s" %(line1.strip(),fp,fp_p,pp_l,pp_l_p,pp_r,pp_r_p)
|
||||
#print >>out_file, "%s\t%d\t%2.2f\t%d\t%2.2f\t%d\t%2.2f" %(line1.strip(),fp,float(fp_p)/abs(end1-start1),pp_l,float(pp_l_p)/abs(end1-start1),pp_r,float(pp_r_p)/abs(end1-start1))
|
||||
"""
|
||||
fo=open("pfct","w")
|
||||
print >>fo, g1
|
||||
print >>fo, g2
|
||||
try:
|
||||
for line in mycoverage([g1,g2]):
|
||||
if type( line ) is GenomicInterval:
|
||||
print >> out_file, "\t".join( line.fields )
|
||||
else:
|
||||
print >> out_file, line
|
||||
|
||||
except ParseError, exc:
|
||||
print >> sys.stderr, "Invalid file format: ", str( exc )
|
||||
|
||||
if g1.skipped > 0:
|
||||
print skipped( g1, filedesc=" of 1st dataset" )
|
||||
|
||||
if g2.skipped > 0:
|
||||
print skipped( g2, filedesc=" of 2nd dataset" )
|
||||
|
||||
"""
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
@@ -1,73 +0,0 @@
|
||||
"""
|
||||
Determine amount of each interval in one set covered by the intervals of
|
||||
another set. Adds two columns to the first input, giving number of bases
|
||||
covered and percent coverage on the second input.
|
||||
"""
|
||||
|
||||
import pkg_resources
|
||||
pkg_resources.require( "bx-python" )
|
||||
|
||||
import psyco_full
|
||||
|
||||
import traceback
|
||||
import fileinput
|
||||
from warnings import warn
|
||||
|
||||
from bx.intervals.io import *
|
||||
from bx.intervals.operations import *
|
||||
|
||||
fo = open("pfc","w")
|
||||
def mycoverage(readers, comments=True):
|
||||
# Read all but first into bitsets and union to one
|
||||
primary = readers[0]
|
||||
intersect = readers[1:]
|
||||
bitsets = intersect[0].binned_bitsets()
|
||||
#print >>fo, primary
|
||||
#print >>fo, intersect
|
||||
#print >>fo, bitsets
|
||||
#print >>fo, primary.keys()
|
||||
#print >>fo, primary.values()
|
||||
#print >>fo, intersect.keys()
|
||||
#print >>fo, intersect.values()
|
||||
print >>fo, bitsets.keys()
|
||||
print >>fo, bitsets.values()
|
||||
intersect = intersect[1:]
|
||||
i=j=0
|
||||
for andset in intersect:
|
||||
print >>fo, "inside j for"
|
||||
print >>fo, andset
|
||||
j = j+1
|
||||
bitset2 = andset.binned_bitsets()
|
||||
for chrom in bitsets:
|
||||
i+=1
|
||||
if chrom not in bitset2: continue
|
||||
bitsets[chrom].ior(bitset2[chrom])
|
||||
print >>fo, "inside i for"
|
||||
print >>fo, i
|
||||
intersect = intersect[1:]
|
||||
print >>fo, j
|
||||
total_features = 0
|
||||
|
||||
# Read remaining intervals and give coverage
|
||||
for interval in primary:
|
||||
if type( interval ) is Header:
|
||||
yield interval
|
||||
if type( interval ) is Comment and comments:
|
||||
yield interval
|
||||
elif type( interval ) == GenomicInterval:
|
||||
chrom = interval.chrom
|
||||
start = int(interval.start)
|
||||
end = int(interval.end)
|
||||
if start > end: warn( "Interval start after end!" )
|
||||
if chrom not in bitsets:
|
||||
bases_covered = 0
|
||||
percent = 0.0
|
||||
else:
|
||||
total_features += 1
|
||||
bases_covered = bitsets[ chrom ].count_range( start, end-start )
|
||||
if (end - start) == 0: percent = 0
|
||||
else: percent = float(bases_covered) / float(end - start)
|
||||
interval.fields.append(str(total_features))
|
||||
interval.fields.append(str(percent))
|
||||
|
||||
yield interval
|
||||
+1
-1
@@ -22,7 +22,7 @@ from bx.intervals.io import *
|
||||
from bx.intervals.operations.merge import *
|
||||
from bx.cookbook import doc_optparse
|
||||
|
||||
from galaxyops import *
|
||||
from galaxy.tools.util.galaxyops import *
|
||||
|
||||
def stop_err(msg):
|
||||
sys.stderr.write(msg)
|
||||
@@ -1,34 +0,0 @@
|
||||
"""
|
||||
Utility functions for galaxyops
|
||||
"""
|
||||
|
||||
from bx.bitset import *
|
||||
from bx.intervals.io import *
|
||||
|
||||
import sys
|
||||
|
||||
def warn( msg ):
|
||||
print >> sys.stderr, msg
|
||||
|
||||
def fail( msg ):
|
||||
print >> sys.stderr, msg
|
||||
sys.exit( 1 )
|
||||
|
||||
# Default chrom, start, end, stran cols for a bed file
|
||||
BED_DEFAULT_COLS = 0, 1, 2, 5
|
||||
|
||||
def parse_cols_arg( cols ):
|
||||
"""Parse a columns command line argument into a four-tuple"""
|
||||
if cols:
|
||||
return map( lambda x: int( x ) - 1, cols.split(",") )
|
||||
else:
|
||||
return BED_DEFAULT_COLS
|
||||
|
||||
def default_printer( stream, exc, obj ):
|
||||
print >> stream, "%d: %s" % ( obj.linenum, obj.current_line )
|
||||
print >> stream, "\tError: %s" % ( str(exc) )
|
||||
|
||||
def skipped( reader, filedesc="" ):
|
||||
first_line, line_contents = reader.skipped_lines[0]
|
||||
return 'Data issue: skipped %d invalid lines%s starting at line #%d which is "%s"' \
|
||||
% ( reader.skipped, filedesc, first_line, line_contents )
|
||||
@@ -1,126 +0,0 @@
|
||||
#!/usr/bin/python2.4
|
||||
|
||||
"""
|
||||
Estimate INDELs for pait-wise alignments.
|
||||
|
||||
usage: %prog maf_input out_file1 out_file2
|
||||
"""
|
||||
|
||||
from __future__ import division
|
||||
import pkg_resources
|
||||
pkg_resources.require( "bx-python" )
|
||||
pkg_resources.require( "lrucache" )
|
||||
try:
|
||||
pkg_resources.require("numpy")
|
||||
pkg_resources.require( "python-lzo" )
|
||||
except:
|
||||
pass
|
||||
|
||||
import psyco_full
|
||||
import sys
|
||||
import os, os.path
|
||||
from UserDict import DictMixin
|
||||
import bx.wiggle
|
||||
from bx.binned_array import BinnedArray, FileBinnedArray
|
||||
from bx.bitset import *
|
||||
from bx.bitset_builders import *
|
||||
from fpconst import isNaN
|
||||
from bx.cookbook import doc_optparse
|
||||
from galaxy.tools.exception_handling import *
|
||||
import bx.align.maf
|
||||
|
||||
def main():
|
||||
# Parsing Command Line here
|
||||
options, args = doc_optparse.parse( __doc__ )
|
||||
|
||||
try:
|
||||
inp_file, out_file1 = args
|
||||
except:
|
||||
print >> sys.stderr, "Tool initialization error."
|
||||
sys.exit()
|
||||
|
||||
try:
|
||||
fin = open(inp_file,'r')
|
||||
except:
|
||||
print >> sys.stderr, "Unable to open input file"
|
||||
sys.exit()
|
||||
try:
|
||||
fout1 = open(out_file1,'w')
|
||||
#fout2 = open(out_file2,'w')
|
||||
except:
|
||||
print >> sys.stderr, "Unable to open output file"
|
||||
sys.exit()
|
||||
|
||||
try:
|
||||
maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
|
||||
except:
|
||||
print >>sys.stderr, "Your MAF file appears to be malformed."
|
||||
sys.exit()
|
||||
maf_count = 0
|
||||
|
||||
print >>fout1, "#Block\tSource\tStart\tEnd\tIndel_length"
|
||||
for block_ind, block in enumerate(maf_reader):
|
||||
if len(block.components) < 2:
|
||||
continue
|
||||
seq1 = block.components[0].text
|
||||
src1 = block.components[0].src
|
||||
start1 = block.components[0].start
|
||||
if len(block.components) == 2:
|
||||
seq2 = block.components[1].text
|
||||
src2 = block.components[1].src
|
||||
start2 = block.components[1].start
|
||||
#for pos in range(len(seq1)):
|
||||
nt_pos1 = start1-1 #position of the nucleotide (without counting gaps)
|
||||
nt_pos2 = start2-1
|
||||
pos = 0 #character column position
|
||||
gaplen1 = 0
|
||||
gaplen2 = 0
|
||||
prev_pos_gap1 = 0
|
||||
prev_pos_gap2 = 0
|
||||
while pos < len(seq1):
|
||||
if prev_pos_gap1 == 0:
|
||||
gaplen1 = 0
|
||||
if prev_pos_gap2 == 0:
|
||||
gaplen2 = 0
|
||||
|
||||
if seq1[pos] == '-':
|
||||
if seq2[pos] != '-':
|
||||
nt_pos2 += 1
|
||||
gaplen1 += 1
|
||||
prev_pos_gap1 = 1
|
||||
#write 2
|
||||
if prev_pos_gap2 == 1:
|
||||
prev_pos_gap2 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2-1,nt_pos2,gaplen2)
|
||||
if pos == len(seq1)-1:
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1,nt_pos1+1,gaplen1)
|
||||
else:
|
||||
if prev_pos_gap1 == 1:
|
||||
prev_pos_gap1 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,gaplen1)
|
||||
elif prev_pos_gap2 == 1:
|
||||
prev_pos_gap2 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2-1,nt_pos2,gaplen2)
|
||||
else:
|
||||
nt_pos1 += 1
|
||||
if seq2[pos] != '-':
|
||||
nt_pos2 += 1
|
||||
#write both
|
||||
if prev_pos_gap1 == 1:
|
||||
prev_pos_gap1 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,gaplen1)
|
||||
elif prev_pos_gap2 == 1:
|
||||
prev_pos_gap2 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2-1,nt_pos2,gaplen2)
|
||||
else:
|
||||
gaplen2 += 1
|
||||
prev_pos_gap2 = 1
|
||||
#write 1
|
||||
if prev_pos_gap1 == 1:
|
||||
prev_pos_gap1 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,gaplen1)
|
||||
if pos == len(seq1)-1:
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2,nt_pos2+1,gaplen2)
|
||||
pos += 1
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
@@ -1,131 +0,0 @@
|
||||
#!/usr/bin/python2.4
|
||||
|
||||
"""
|
||||
Estimate INDEL rates.
|
||||
|
||||
usage: %prog maf_input out_file1 out_file2
|
||||
"""
|
||||
|
||||
from __future__ import division
|
||||
import pkg_resources
|
||||
pkg_resources.require( "bx-python" )
|
||||
pkg_resources.require( "lrucache" )
|
||||
try:
|
||||
pkg_resources.require("numpy")
|
||||
pkg_resources.require( "python-lzo" )
|
||||
except:
|
||||
pass
|
||||
|
||||
import psyco_full
|
||||
import sys
|
||||
import os, os.path
|
||||
from UserDict import DictMixin
|
||||
import bx.wiggle
|
||||
from bx.binned_array import BinnedArray, FileBinnedArray
|
||||
from bx.bitset import *
|
||||
from bx.bitset_builders import *
|
||||
from fpconst import isNaN
|
||||
from bx.cookbook import doc_optparse
|
||||
from galaxy.tools.exception_handling import *
|
||||
import bx.align.maf
|
||||
|
||||
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, out_file1 = args
|
||||
except:
|
||||
doc_optparse.exception()
|
||||
|
||||
try:
|
||||
fin = open(inp_file,'r')
|
||||
except:
|
||||
print >> sys.stderr, "Unable to open input file"
|
||||
sys.exit()
|
||||
try:
|
||||
fout1 = open(out_file1,'w')
|
||||
#fout2 = open(out_file2,'w')
|
||||
except:
|
||||
print >> sys.stderr, "Unable to open output file"
|
||||
sys.exit()
|
||||
|
||||
try:
|
||||
maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
|
||||
except:
|
||||
print >>sys.stderr, "Your MAF file appears to be malformed."
|
||||
sys.exit()
|
||||
maf_count = 0
|
||||
|
||||
print >>fout1, "#Block\tSource\tStart\tEnd\tEvent"
|
||||
for block_ind, block in enumerate(maf_reader):
|
||||
if len(block.components) != 2:
|
||||
continue
|
||||
seqs = []
|
||||
srcs = []
|
||||
starts = []
|
||||
gaplens = []
|
||||
gapstatus = []
|
||||
starts.append(block.components[0].start)
|
||||
for seq_num in range(len(block.components)):
|
||||
seqs.append(block.components[seq_num].text)
|
||||
srcs.append(block.components[seq_num].src)
|
||||
starts.append(block.components[seq_num].start)
|
||||
gaplens.append(0)
|
||||
gapstatus.append(0)
|
||||
|
||||
pos = 0 #character column position
|
||||
nt_pos1 = 0 #nt positions
|
||||
nt_pos2 = 0
|
||||
while pos < len(seqs[0]):
|
||||
for j,elem in enumerate(seqs):
|
||||
if gapstatus[j] == 0:
|
||||
gaplens[j] = 0
|
||||
if seqs[0][pos] == '-':
|
||||
next = pos+1
|
||||
leng = 1
|
||||
while next < len(seqs[0]):
|
||||
if seqs[0][next] == '-':
|
||||
leng += 1
|
||||
|
||||
if seq2[pos] != '-':
|
||||
nt_pos2 += 1
|
||||
gaplen1 += 1
|
||||
prev_pos_gap1 = 1
|
||||
#write 2
|
||||
if prev_pos_gap2 == 1:
|
||||
prev_pos_gap2 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2-1,nt_pos2,gaplen2)
|
||||
if pos == len(seq1)-1:
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1,nt_pos1+1,gaplen1)
|
||||
else:
|
||||
if prev_pos_gap1 == 1:
|
||||
prev_pos_gap1 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,gaplen1)
|
||||
elif prev_pos_gap2 == 1:
|
||||
prev_pos_gap2 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2-1,nt_pos2,gaplen2)
|
||||
else:
|
||||
nt_pos1 += 1
|
||||
if seq2[pos] != '-':
|
||||
nt_pos2 += 1
|
||||
#write both
|
||||
if prev_pos_gap1 == 1:
|
||||
prev_pos_gap1 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,gaplen1)
|
||||
elif prev_pos_gap2 == 1:
|
||||
prev_pos_gap2 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2-1,nt_pos2,gaplen2)
|
||||
else:
|
||||
gaplen2 += 1
|
||||
prev_pos_gap2 = 1
|
||||
#write 1
|
||||
if prev_pos_gap1 == 1:
|
||||
prev_pos_gap1 = 0
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src1,nt_pos1-1,nt_pos1,gaplen1)
|
||||
if pos == len(seq1)-1:
|
||||
print >>fout1,"%d\t%s\t%s\t%s\t%s" %(block_ind+1,src2,nt_pos2,nt_pos2+1,gaplen2)
|
||||
pos += 1
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
@@ -1,24 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
import sys, re, os, tempfile
|
||||
|
||||
qual_dir = "/depot/data2/galaxy/mm8/align/multiz17way"
|
||||
fout = open("ploc","w")
|
||||
os.chdir(qual_dir)
|
||||
|
||||
tmpfile = tempfile.NamedTemporaryFile()
|
||||
cmdline = "ls " + "*.lzo | cat >> " + tmpfile.name
|
||||
os.system (cmdline)
|
||||
|
||||
fstr = "17-way multiZ (mm8)\t17_WAY_MULTIZ_mm8\tmm8\t"
|
||||
|
||||
for j,qual_file in enumerate(tmpfile.readlines()):
|
||||
if j!=0:
|
||||
fstr = fstr + ',' + qual_dir + '/' + qual_file.strip()
|
||||
else:
|
||||
fstr = fstr + qual_dir + '/' + qual_file.strip()
|
||||
|
||||
print >>fout, fstr
|
||||
print fstr
|
||||
|
||||
os.system("echo '%s' | cat >> /depot/data2/galaxy/maf_index.loc" %(fstr))
|
||||
@@ -1,30 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
import sys, re, os, tempfile
|
||||
|
||||
qual_dir = "/home/gua110/Desktop/rhesus_quality_scores/chr"
|
||||
qual_file= open("/home/gua110/Desktop/rhesus_quality_scores/rheMac2.qual.qa", "r")
|
||||
|
||||
qual_file_contents = qual_file.read(1000000000)
|
||||
|
||||
while qual_file_contents != "":
|
||||
contents_list = qual_file_contents.split(">")
|
||||
os.chdir(qual_dir)
|
||||
print "len_contents_list", len(contents_list)
|
||||
if len(contents_list) == 1:
|
||||
os.system("echo %s | cat >> %s.qa" %(contents_list, prev_file))
|
||||
else:
|
||||
#print len(contents_list[0])
|
||||
#print len(contents_list[1])
|
||||
for elem in contents_list:
|
||||
if elem == '':
|
||||
continue
|
||||
if elem.startswith("chr"):
|
||||
elems = elem.replace("\r","\n").split("\n")
|
||||
cmdline = "echo %s | cat >> %s.qa" %(elems[1:], elems[0])
|
||||
os.system("echo >%s\n%s | cat >> %s.qa" %(elems[0], elems[1:], elems[0]))
|
||||
else:
|
||||
os.system("echo %s | cat >> %s.qa" %(elem, prev_file))
|
||||
prev_file = elems[0]
|
||||
qual_file_contents = qual_file.read(1000000000)
|
||||
|
||||
+1
-1
@@ -11,7 +11,7 @@ import sys, sets, re, os
|
||||
|
||||
import pkg_resources; pkg_resources.require( "bx-python" )
|
||||
from bx.cookbook import doc_optparse
|
||||
from galaxyops import *
|
||||
from galaxy.tools.util.galaxyops import *
|
||||
|
||||
def main():
|
||||
# Parsing Command Line here
|
||||
Reference in New Issue
Block a user