| Next changeset 1:64f5401327e8 (2014-10-30) |
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Commit message:
Imported from capsule None |
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added:
quality_filter.py quality_filter.xml test-data/6.maf test-data/6_quality_filter.maf tool_dependencies.xml |
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| diff -r 000000000000 -r 8d65bbc52dfe quality_filter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/quality_filter.py Tue Apr 01 10:52:42 2014 -0400 |
| [ |
| b'@@ -0,0 +1,238 @@\n+#!/usr/bin/env python\n+#Guruprasad Ananda\n+"""\n+Filter based on nucleotide quality (PHRED score).\n+\n+usage: %prog input out_file primary_species mask_species score mask_char mask_region mask_region_length\n+"""\n+\n+\n+from __future__ import division\n+from galaxy import eggs\n+import pkg_resources\n+pkg_resources.require( "lrucache" )\n+import numpy\n+\n+import sys\n+import os, os.path\n+from UserDict import DictMixin\n+from bx.binned_array import FileBinnedArray\n+from bx.bitset import *\n+from bx.bitset_builders import *\n+from bx.cookbook import doc_optparse\n+from galaxy.tools.exception_handling import *\n+import bx.align.maf\n+\n+class FileBinnedArrayDir( DictMixin ):\n+ """\n+ Adapter that makes a directory of FileBinnedArray files look like\n+ a regular dict of BinnedArray objects.\n+ """\n+ def __init__( self, dir ):\n+ self.dir = dir\n+ self.cache = dict()\n+ def __getitem__( self, key ):\n+ value = None\n+ if key in self.cache:\n+ value = self.cache[key]\n+ else:\n+ fname = os.path.join( self.dir, "%s.qa.bqv" % key )\n+ if os.path.exists( fname ):\n+ value = FileBinnedArray( open( fname ) )\n+ self.cache[key] = value\n+ if value is None:\n+ raise KeyError( "File does not exist: " + fname )\n+ return value\n+\n+def stop_err(msg):\n+ sys.stderr.write(msg)\n+ sys.exit()\n+\n+def load_scores_ba_dir( dir ):\n+ """\n+ Return a dict-like object (keyed by chromosome) that returns\n+ FileBinnedArray objects created from "key.ba" files in `dir`\n+ """\n+ return FileBinnedArrayDir( dir )\n+\n+def bitwise_and ( string1, string2, maskch ):\n+ result = []\n+ for i, ch in enumerate(string1):\n+ try:\n+ ch = int(ch)\n+ except:\n+ pass\n+ if string2[i] == \'-\':\n+ ch = 1\n+ if ch and string2[i]:\n+ result.append(string2[i])\n+ else:\n+ result.append(maskch)\n+ return \'\'.join(result)\n+\n+def main():\n+ # Parsing Command Line here\n+ options, args = doc_optparse.parse( __doc__ )\n+ \n+ try:\n+ #chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )\n+ inp_file, out_file, pri_species, mask_species, qual_cutoff, mask_chr, mask_region, mask_length, loc_file = args\n+ qual_cutoff = int(qual_cutoff)\n+ mask_chr = int(mask_chr)\n+ mask_region = int(mask_region)\n+ if mask_region != 3:\n+ mask_length = int(mask_length)\n+ else:\n+ mask_length_r = int(mask_length.split(\',\')[0])\n+ mask_length_l = int(mask_length.split(\',\')[1])\n+ except:\n+ stop_err( "Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset." )\n+ \n+ if pri_species == \'None\':\n+ stop_err( "No primary species selected, try again by selecting at least one primary species." )\n+ if mask_species == \'None\':\n+ stop_err( "No mask species selected, try again by selecting at least one species to mask." )\n+\n+ mask_chr_count = 0\n+ mask_chr_dict = {0:\'#\', 1:\'$\', 2:\'^\', 3:\'*\', 4:\'?\', 5:\'N\'}\n+ mask_reg_dict = {0:\'Current pos\', 1:\'Current+Downstream\', 2:\'Current+Upstream\', 3:\'Current+Both sides\'}\n+\n+ #ensure dbkey is present in the twobit loc file\n+ try:\n+ pspecies_all = pri_species.split(\',\')\n+ pspecies_all2 = pri_species.split(\',\')\n+ pspecies = []\n+ filepaths = []\n+ for line in open(loc_file):\n+ if pspecies_all2 == []:\n+ break\n+ if line[0:1] == "#":\n+ continue\n+ fields = line.split(\'\\t\')\n+ try:\n+ build = fields[0]\n+ for i, dbkey in enumerate(pspecies_all2):\n+ if dbkey == build:\n+ pspecies.append(build)\n+ filepaths.append(fields[1])\n+ del pspecies_all2[i]\n+ '..b'ex(dbkey)\n+ sequence = block.components[seq].text\n+ s_start = block.components[seq].start\n+ size = len(sequence) #this includes the gaps too\n+ status_str = \'1\'*size\n+ status_list = list(status_str)\n+ if status_strings == []:\n+ status_strings.append(status_str)\n+ ind = 0\n+ s_end = block.components[seq].end\n+ #Get scores for the entire sequence\n+ try:\n+ scores = scores_by_chrom[index][chr][s_start:s_end]\n+ except:\n+ continue\n+ pos = 0\n+ while pos < (s_end-s_start):\n+ if sequence[ind] == \'-\': #No score for GAPS\n+ ind += 1\n+ continue\n+ score = scores[pos]\n+ if score < qual_cutoff:\n+ score = 0\n+ \n+ if not(score):\n+ if mask_region == 0: #Mask Corresponding position only\n+ status_list[ind] = \'0\'\n+ ind += 1\n+ pos += 1\n+ elif mask_region == 1: #Mask Corresponding position + downstream neighbors\n+ for n in range(mask_length+1):\n+ try:\n+ status_list[ind+n] = \'0\'\n+ except:\n+ pass\n+ ind = ind + mask_length + 1\n+ pos = pos + mask_length + 1\n+ elif mask_region == 2: #Mask Corresponding position + upstream neighbors\n+ for n in range(mask_length+1):\n+ try:\n+ status_list[ind-n] = \'0\'\n+ except:\n+ pass\n+ ind += 1\n+ pos += 1\n+ elif mask_region == 3: #Mask Corresponding position + neighbors on both sides\n+ for n in range(-mask_length_l, mask_length_r+1):\n+ try:\n+ status_list[ind+n] = \'0\'\n+ except:\n+ pass\n+ ind = ind + mask_length_r + 1\n+ pos = pos + mask_length_r + 1\n+ else:\n+ pos += 1\n+ ind += 1\n+ \n+ status_strings.append(\'\'.join(status_list))\n+ \n+ if status_strings == []: #this block has no primary species\n+ continue\n+ output_status_str = status_strings[0]\n+ for stat in status_strings[1:]:\n+ try:\n+ output_status_str = bitwise_and (status_strings[0], stat, \'0\')\n+ except Exception, e:\n+ break\n+ \n+ for seq in range (len(block.components)):\n+ src = block.components[seq].src\n+ dbkey = src.split(\'.\')[0]\n+ if dbkey not in mask_species.split(\',\'):\n+ continue\n+ sequence = block.components[seq].text\n+ sequence = bitwise_and (output_status_str, sequence, mask_chr_dict[mask_chr])\n+ block.components[seq].text = sequence\n+ mask_chr_count += output_status_str.count(\'0\')\n+ maf_writer.write(block)\n+ maf_count += 1\n+ \n+ maf_reader.close()\n+ maf_writer.close()\n+ print "No. of blocks = %d; No. of masked nucleotides = %s; Mask character = %s; Mask region = %s; Cutoff used = %d" % (maf_count, mask_chr_count, mask_chr_dict[mask_chr], mask_reg_dict[mask_region], qual_cutoff)\n+\n+\n+if __name__ == "__main__":\n+ main()\n' |
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| diff -r 000000000000 -r 8d65bbc52dfe quality_filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/quality_filter.xml Tue Apr 01 10:52:42 2014 -0400 |
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| @@ -0,0 +1,119 @@ +<tool id="qualityFilter" name="Filter nucleotides" version="1.0.1"> + <description> based on quality scores</description> + <requirements> + <requirement type="package" version="0.7.1">bx-python</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + </requirements> + <command interpreter="python"> + quality_filter.py + $input + $out_file1 + $primary_species + $mask_species + $score + $mask_char + ${mask_region.region} + #if $mask_region.region == "3" + ${mask_region.lengthr},${mask_region.lengthl} + #elif $mask_region.region == "0" + 1 + #else + ${mask_region.length} + #end if + ${GALAXY_DATA_INDEX_DIR}/quality_scores.loc + </command> + <inputs> + <param format="maf" name="input" type="data" label="Select data"/> + <param name="primary_species" type="select" label="Use quality scores of" display="checkboxes" multiple="true"> + <options> + <filter type="data_meta" ref="input" key="species" /> + </options> + </param> + <param name="mask_species" type="select" label="Mask Species" display="checkboxes" multiple="true"> + <options> + <filter type="data_meta" ref="input" key="species" /> + </options> + </param> + <param name="score" size="10" type="integer" value="20" label="Quality score cut-off" help="Cut-off value of 20 means mask all nucleotides having quality score less than or equal to 20"/> + <param name="mask_char" size="5" type="select" label="Mask character"> + <option value="0" selected="true">#</option> + <option value="1">$</option> + <option value="2">^</option> + <option value="3">*</option> + <option value="4">?</option> + <option value="5">N</option> + </param> + <conditional name="mask_region"> + <param name="region" type="select" label="Mask region"> + <option value="0" selected="true">Only the corresponding nucleotide </option> + <option value="1">Corresponding column + right-side neighbors</option> + <option value="2">Corresponding column + left-side neighbors</option> + <option value="3">Corresponding column + neighbors on both sides</option> + </param> + <when value="0"> + </when> + <when value="1"> + <param name="length" size="10" type="integer" value="2" label="Number of right-side neighbors"/> + </when> + <when value="2"> + <param name="length" size="10" type="integer" value="2" label="Number of left-side neighbors"/> + </when> + <when value="3"> + <param name="lengthr" size="10" type="integer" value="2" label="Number of neighbors on right-side" /> + <param name="lengthl" size="10" type="integer" value="2" label="Number of neighbors on left-side" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="maf" name="out_file1" metadata_source="input"/> + </outputs> + <requirements> + <requirement type="python-module">numpy</requirement> + </requirements> + <tests> + <test> + <param name="input" value="6.maf"/> + <param name="primary_species" value="panTro2"/> + <param name="mask_species" value="hg18"/> + <param name="score" value="50"/> + <param name="mask_char" value="0"/> + <param name="region" value="0" /> + <output name="out_file1" file="6_quality_filter.maf"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What it does** + +This tool takes a MAF file as input and filters nucleotides in every alignment block of the MAF file based on their quality/PHRED scores. + +----- + +.. class:: warningmark + +**Note** + +Any block/s not containing the primary species (species whose quality scores is to be used), will be omitted. +Also, any primary species whose quality scores are not available in Galaxy will be considered as a non-primary species. This info will appear as a message in the job history panel. + +----- + +**Example** + +- For the following alignment block:: + + a score=4050.0 + s hg18.chrX 3719221 48 - 154913754 tattttacatttaaaataaatatgtaaatatatattttatatttaaaa + s panTro2.chrX 3560945 48 - 155361357 tattttatatttaaaataaagatgtaaatatatattttatatttaaaa + +- running this tool with **Primary species as panTro2**, **Mask species as hg18, panTro2**, **Quality cutoff as 20**, **Mask character as #** and **Mask region as only the corresponding position** will return:: + + a score=4050.0 + s hg18.chrX 3719221 48 - 154913754 ###tttac#####a###a#atatgtaaat###tattt#####ttaaaa + s panTro2.chrX 3560945 48 - 155361357 ###tttat#####a###a#agatgtaaat###tattt#####ttaaaa + + where, the positions containing # represent panTro2 nucleotides having quality scores less than 20. + </help> +</tool> |
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| diff -r 000000000000 -r 8d65bbc52dfe test-data/6.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6.maf Tue Apr 01 10:52:42 2014 -0400 |
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| b'@@ -0,0 +1,57 @@\n+##maf version=1\n+a score=356676.0\n+s hg18.chr1 2817 1438 + 247249719 GTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGTCGACAGACAGGGGCTGGAGAAGGGGAGAAGAGGAAAGTGAGGTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGGCCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATT--TGTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTTGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAG \n+s panTro2.chr15 16051 1440 - 100063422 GTCATCCCCTTCACTCCCAGCTCTGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGTGGACAGACAGGCGCTGGAGAAGGGGAGAAGAGGAAAGGGGGGCTGCCTGCCCTGTCTCCCACCTGAGGCTGAGGAAGGAGAGGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCCTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAATGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACAAGCTGTTGGCCTGGATCTGAGCCCTCGTGGAGCTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCAGTCCTGCCTTTTCCTTTCCCGAGAGGCTCCACCACCCCGAGATCGCACTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGCGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCAAAGAAATGGTGAGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCAGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTCTGTCCTGCCCACCTTCTAAGAAGCGAGACGGAGGACACCCATCTGCTTCTGCCCTTTCCATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCTATTTAAAAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCACTTCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACTACTTGAGCAAACTTGAAGACATCTTCAACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTCGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGCACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGGTCCTTAATTAAAAG \n+\n+a score=33380.0\n+s hg18.chr1 4393 135 + 247249719 GTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTG \n+s panTro2.chr15 17634 135 - 100063422 GTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAGGGAAGCAGGTCTCAGCAGCTTGTCCTGGCTGTGTCCGTGTCAGAGCAACGGCCCAAGTCTG \n+\n+a score=364526.0\n+s hg18.chr1 4528 1436 + 247249719 GGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGGACAGAATTACAAGGTGCTGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGCGACCGGTGACTCCCTGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCACTGATGAGACAGCGGCTGTTTGA'..b'ttctctcctctgtcttttcccaccaagtgaggatgcgaagagaaggtggctgtctgcaaaccaggaagagagccctcaccgggaacccgtccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagtcgcccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGCAATATCTGAGTGGCTTAAGGTACTCAGGACACAACAAAGGAGAAATGTCCCATGCACAAGGTGCACCCATGCCTGGGTAAAGCAGCCTGGCACAGAGGGAAGCACACAGGCTCAGggatctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgtgcttgccctgcctccttttgagggctgtagagaaaagatgtcaaagtattttgtaATCTggctgggcgtggtggctcatgcctgtaatcctagcactttggtaggctgacgcgagaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgaggcgggaggatcacttgagcttgggagatcgaggctgcagtgagctatgattgtaccactgcactccaggctgggcgacagagagagaccctgtctcagaaaaaaaaaaaaaaGTACTTTGTAATCTGTAAGGTTTATTTCAACACACACAAAAAAAGTGTATATGCTCCACGATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGCACTGCTAGGCACCACCC \n+s panTro2.chrUn 57103829 1814 - 58616431 tgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtagcgatggcggcgcaacagtgtgaatctacttaatcccactgaactgtatgcttaaaaatggtttagacggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaatacaggatgcccagttagtttgaattttagataaacaacgaataatttcgtagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcaaaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTGACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCTTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCACTGGCTGCAGCGTGTGGTCCCCTTACCAGAGGTAAGGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaattcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaattacggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagagcattgtctctctgtctccctctc-----------------------tctctctatgtcatttctctctct----ctatctca--tttctctctctctctctctctcctctgtcttttcccaccaagtgaggatgcgaagagaaggtggctgtctgcaaaccaggaagagagccctcaccaggaacccgtccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagtcgcccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGGAATATCTGAGTGGCTTAATGTACTCAGGACACAACAA---AGAAATGTCCCATGCACAAGGTGCACCCATGCCtgggtaaagcagcctggcacagagggaagcacacaggctcagggctctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgagcttgccctgcctccttctgagggctgtagagaaaagatgtcaaagtattttgtaatctggctgggcgtggtggctcatgcctgtaatcccagcactttggtaggctgacgcgagaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgaggcgggaggatcacttgagcttgggagatcgaggctgcagtgagctatgattgtaccactgcactccaggctgggcgacagagagagaccctgtctcag--aaaaaagaaaaagtactttgtaatctgtaaggtttatttcaacacACACAAAAAAAGTGTATATGCTCCACGATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGCGCTGCTGGGCACCACCC \n+\n+a score=97796.0\n+s hg18.chr1 21738 409 + 247249719 CCAGTTCTAGAATCACACCAGCCAGTTCACCCTCCAGATGGTTCACCCTCAACTTCATAAAAGTTCCCTACCTAATCTACT---GACAGGCTCATCCCCGACCTAATTTTAAAGATTTCCTAGGA----------------------------------GCTGCAGTGGGAATCCTGGACCTCAGCCTGGACAAAGAACAGCTGCAGGTCATTCTCATGTGTGGACACAGAAGCTCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAGCGGGCCTGGGAA-TTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAAGCCCCGATCTACAGGAAGAAAACTGGAA \n+s panTro2.chrUn 57107006 446 - 58616431 CCAGTTCTAGAACCAGACCAGACAGTTCACCCTCCAGACGGTTCACCCTCAACTGTATAAAAGTTCTCTACCTAATCTACTACTGACAGACTCATCTCAGACCTAATTTTAAAGATTTCCTAGGAACTGAATTGCAAAAACTTTTACCCTCACCCTAGAGCTGCAATGGGAATCCTG-ACCTCAGCGTAGACAAAGAAAAGCTGCAGGTCATTCTCATGTGTGGACACGGAAGCCCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAGTGGGCCTGGGAAATTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAGGCCCCAATCTACAGGAAGAAAACTGGAA \n+\n+a score=7233.0\n+s hg18.chr1 22147 35 + 247249719 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT \n+s panTro2.chrUn 57107452 35 - 58616431 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT \n+\n' |
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| diff -r 000000000000 -r 8d65bbc52dfe test-data/6_quality_filter.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6_quality_filter.maf Tue Apr 01 10:52:42 2014 -0400 |
| b |
| b'@@ -0,0 +1,57 @@\n+##maf version=1\n+a score=356676.0\n+s hg18.chr1 2817 1438 + 247249719 #############################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################--################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################# \n+s panTro2.chr15 16051 1440 - 100063422 GTCATCCCCTTCACTCCCAGCTCTGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGTGGACAGACAGGCGCTGGAGAAGGGGAGAAGAGGAAAGGGGGGCTGCCTGCCCTGTCTCCCACCTGAGGCTGAGGAAGGAGAGGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCCTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAATGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACAAGCTGTTGGCCTGGATCTGAGCCCTCGTGGAGCTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCAGTCCTGCCTTTTCCTTTCCCGAGAGGCTCCACCACCCCGAGATCGCACTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGCGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCAAAGAAATGGTGAGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCAGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTCTGTCCTGCCCACCTTCTAAGAAGCGAGACGGAGGACACCCATCTGCTTCTGCCCTTTCCATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCTATTTAAAAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCACTTCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACTACTTGAGCAAACTTGAAGACATCTTCAACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTCGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGCACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGGTCCTTAATTAAAAG \n+\n+a score=33380.0\n+s hg18.chr1 4393 135 + 247249719 ####################################################################################################################################### \n+s panTro2.chr15 17634 135 - 100063422 GTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAGGGAAGCAGGTCTCAGCAGCTTGTCCTGGCTGTGTCCGTGTCAGAGCAACGGCCCAAGTCTG \n+\n+a score=364526.0\n+s hg18.chr1 4528 1436 + 247249719 ########################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################'..b'ttctctcctctgtcttttc#cacca#gtgaggatgcgaagagaaggtggctgtctgc#a##c##gaagagag#c#tcac#ggg#ac##gtc###############a###g#######################g#g#ga###a###########a#######cca#t##################################################################################################AGG###################G############################################C####G################################c#t#############################################################################################################################################################################################################################################################################################################################################################################################################aa###########################################################TATATGC##############################CA##############################CAC#######CTGC#A##CACCACCC \n+s panTro2.chrUn 57103829 1814 - 58616431 tgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtagcgatggcggcgcaacagtgtgaatctacttaatcccactgaactgtatgcttaaaaatggtttagacggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaatacaggatgcccagttagtttgaattttagataaacaacgaataatttcgtagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcaaaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTGACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCTTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCACTGGCTGCAGCGTGTGGTCCCCTTACCAGAGGTAAGGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaattcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaattacggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagagcattgtctctctgtctccctctc-----------------------tctctctatgtcatttctctctct----ctatctca--tttctctctctctctctctctcctctgtcttttcccaccaagtgaggatgcgaagagaaggtggctgtctgcaaaccaggaagagagccctcaccaggaacccgtccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagtcgcccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGGAATATCTGAGTGGCTTAATGTACTCAGGACACAACAA---AGAAATGTCCCATGCACAAGGTGCACCCATGCCtgggtaaagcagcctggcacagagggaagcacacaggctcagggctctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgagcttgccctgcctccttctgagggctgtagagaaaagatgtcaaagtattttgtaatctggctgggcgtggtggctcatgcctgtaatcccagcactttggtaggctgacgcgagaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgaggcgggaggatcacttgagcttgggagatcgaggctgcagtgagctatgattgtaccactgcactccaggctgggcgacagagagagaccctgtctcag--aaaaaagaaaaagtactttgtaatctgtaaggtttatttcaacacACACAAAAAAAGTGTATATGCTCCACGATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGCGCTGCTGGGCACCACCC \n+\n+a score=97796.0\n+s hg18.chr1 21738 409 + 247249719 #################CCA##CA###########AGA###########################################---################ACC#AATTT################----------------------------------##################G#########################G#A######TCT#####G#################C#######TGC#######CTGGGCTGA###########AA-TTAAGGC###AGGGTTGG#########G############TT###ACATCCCCCA#CCTCCTG##TTTGCCA#####CAAGAGCA#G#A#TTTA#########G#####G####GAAGA##AT#T##CAGGGTGTCCTA#GCCCCGATCTACAGGAAGAAAACT#GA# \n+s panTro2.chrUn 57107006 446 - 58616431 CCAGTTCTAGAACCAGACCAGACAGTTCACCCTCCAGACGGTTCACCCTCAACTGTATAAAAGTTCTCTACCTAATCTACTACTGACAGACTCATCTCAGACCTAATTTTAAAGATTTCCTAGGAACTGAATTGCAAAAACTTTTACCCTCACCCTAGAGCTGCAATGGGAATCCTG-ACCTCAGCGTAGACAAAGAAAAGCTGCAGGTCATTCTCATGTGTGGACACGGAAGCCCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAGTGGGCCTGGGAAATTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAGGCCCCAATCTACAGGAAGAAAACTGGAA \n+\n+a score=7233.0\n+s hg18.chr1 22147 35 + 247249719 #####ACTG#GG##T##GTTTAAGATGTTCCTACT \n+s panTro2.chrUn 57107452 35 - 58616431 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT \n+\n' |
| b |
| diff -r 000000000000 -r 8d65bbc52dfe tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 01 10:52:42 2014 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bx-python" version="0.7.1"> + <repository changeset_revision="41eb9d9f667d" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |