| Previous changeset 4:be070a68521e (2012-10-18) Next changeset 6:f201e8c6e004 (2014-07-07) |
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Commit message:
Uploaded |
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modified:
CAPS2gff.sh design_primers.py design_primers.xml find_CAPS.xml gsmapper2gff.sh parse_primersearch.pl uniq.xml vcf_gff.py vcf_gff.xml |
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added:
README.md ipcress.xml ipcress_gff.xml run_p3.py test-data/find_caps_output.txt test-data/freebayes_out.vcf test-data/freebayes_vcf_to_gff_output.gff test-data/ipcress.out test-data/ipcress_gff.out test-data/ipcress_test_input.txt test-data/mpileup_out.vcf test-data/mpileup_vcf_to_gff_output.gff test-data/targets test-data/targets.fasta test-data/targets.gff umelt_service.py vcf2gvf.py vcf2gvf.sh vcf2gvf.xml |
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removed:
Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga |
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| diff -r be070a68521e -r b321e0517be3 CAPS2gff.sh --- a/CAPS2gff.sh Thu Oct 18 19:47:07 2012 -0400 +++ b/CAPS2gff.sh Thu May 22 20:30:19 2014 -0400 |
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| @@ -1,5 +1,7 @@ #!/bin/sh ##convert output of CAPS detection tool to GFF3 +## usage +# sh CAPS2gff.sh <input tabular CAPS output> <output file> #Copyright 2012 John McCallum #New Zealand Institute for Plant and Food Research |
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| diff -r be070a68521e -r b321e0517be3 Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga --- a/Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga Thu Oct 18 19:47:07 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,273 +0,0 @@\n-{\n- "a_galaxy_workflow": "true", \n- "annotation": "", \n- "format-version": "0.1", \n- "name": "CAPS Marker Design from VCF", \n- "steps": {\n- "0": {\n- "annotation": "", \n- "id": 0, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Multi fasta Dataset"\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 214, \n- "top": 225\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Multi fasta Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": []\n- }, \n- "1": {\n- "annotation": "", \n- "id": 1, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input VCF Dataset"\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 174, \n- "top": 592\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input VCF Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": []\n- }, \n- "2": {\n- "annotation": "", \n- "id": 2, \n- "input_connections": {\n- "inputVcf": {\n- "id": 1, \n- "output_name": "output"\n- }\n- }, \n- "inputs": [], \n- "name": "Convert vcf to gff", \n- "outputs": [\n- {\n- "name": "outputfile", \n- "type": "gff3"\n- }\n- ], \n- "position": {\n- "left": 460.99998474121094, \n- "top": 568\n- }, \n- "post_job_actions": {}, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/vcf2gff_1/1.0.0", \n- "tool_state": "{\\"inputVcf\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"__page__\\": 0}", \n- "tool_version": "1.0.0", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "3": {\n- "annotation": "Detect resitriction polymorphisms", \n- "id": 3, \n- "input_connections": {\n- "inputFasta": {\n- "id": 0, \n- "output_name": "output"\n- }, \n- "inputSNPGff3File": {\n- "id": 2, \n- "output_name": "outputfile"\n- }\n- }, \n- "inputs": [], \n- "name": "CAPS Detection", \n- "outputs": [\n- {\n- "name": "outputfile", \n- "type": "interval"\n- }\n- ], \n- "position": {\n- "left": 646.99998474121094, \n- "top": 382\n- }, \n- "post_job_actions": {}, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/CAPS_Marker_Design_2/1.0.0", \n- "tool_state": "{\\"inputFasta\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"inputSNPGff3File\\": \\"null\\", \\"__page__\\": 0}", \n- "tool_version": "1.0.0", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "4": {\n- "annotation": "get feature I'..b'{\n- "name": "primer_outputfile", \n- "type": "tabular"\n- }\n- ], \n- "position": {\n- "left": 1186, \n- "top": 382\n- }, \n- "post_job_actions": {\n- "RenameDatasetActionprimer_outputfile": {\n- "action_arguments": {\n- "newname": "PrimerPairs"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "primer_outputfile"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/Genetic_Marker_Design_2/1.0.0", \n- "tool_state": "{\\"__page__\\": 0, \\"inputTargetfile\\": \\"null\\", \\"inputfastaFile\\": \\"null\\", \\"min_size\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"inputSNPfile\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"max_size\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n- "tool_version": "1.0.0", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "6": {\n- "annotation": "", \n- "id": 6, \n- "input_connections": {\n- "input": {\n- "id": 5, \n- "output_name": "primer_outputfile"\n- }\n- }, \n- "inputs": [], \n- "name": "Select", \n- "outputs": [\n- {\n- "name": "out_file1", \n- "type": "input"\n- }\n- ], \n- "position": {\n- "left": 1406, \n- "top": 382\n- }, \n- "post_job_actions": {\n- "RenameDatasetActionout_file1": {\n- "action_arguments": {\n- "newname": "SuccessfulDesignSets"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "out_file1"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "Grep1", \n- "tool_state": "{\\"__page__\\": 0, \\"input\\": \\"null\\", \\"invert\\": \\"\\\\\\"true\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"pattern\\": \\"\\\\\\"NONE\\\\\\"\\"}", \n- "tool_version": "1.0.1", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "7": {\n- "annotation": "", \n- "id": 7, \n- "input_connections": {\n- "inputFile": {\n- "id": 6, \n- "output_name": "out_file1"\n- }\n- }, \n- "inputs": [], \n- "name": "Unique", \n- "outputs": [\n- {\n- "name": "outputfile", \n- "type": "txt"\n- }\n- ], \n- "position": {\n- "left": 1625.9999389648438, \n- "top": 382\n- }, \n- "post_job_actions": {\n- "RenameDatasetActionoutputfile": {\n- "action_arguments": {\n- "newname": "UniquePrimerSets"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "outputfile"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/uni_Mask_1/1.0.0", \n- "tool_state": "{\\"__page__\\": 0, \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"inputFile\\": \\"null\\"}", \n- "tool_version": "1.0.0", \n- "type": "tool", \n- "user_outputs": []\n- }\n- }\n-}\n\\ No newline at end of file\n' |
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| diff -r be070a68521e -r b321e0517be3 Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga --- a/Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga Thu Oct 18 19:47:07 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,401 +0,0 @@\n-{\n- "a_galaxy_workflow": "true", \n- "annotation": "", \n- "format-version": "0.1", \n- "name": "CAPS Marker Development from 454 Read Mapping", \n- "steps": {\n- "0": {\n- "annotation": "", \n- "id": 0, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Reference sequences"\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 122.80303955078125, \n- "top": 119.77274131774902\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Reference sequences\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": []\n- }, \n- "1": {\n- "annotation": "Reads to map", \n- "id": 1, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "Reads to map", \n- "name": "SFF File "\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 104.6212158203125, \n- "top": 313.95454406738281\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"SFF File \\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": []\n- }, \n- "2": {\n- "annotation": "barcode, vector or adapter sequences to trim", \n- "id": 2, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "barcode, vector or adapter sequences to trim", \n- "name": "Trimming file"\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 195.727294921875, \n- "top": 544.8787841796875\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Trimming file\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": []\n- }, \n- "3": {\n- "annotation": "", \n- "id": 3, \n- "input_connections": {\n- "ref_inputs_0|ref_input": {\n- "id": 0, \n- "output_name": "output"\n- }, \n- "sff_inputs_0|sff_input": {\n- "id": 1, \n- "output_name": "output"\n- }, \n- "vt": {\n- "id": 2, \n- "output_name": "output"\n- }\n- }, \n- "inputs": [], \n- "name": "runMapping", \n- "outputs": [\n- {\n- "name": "newbler_metrics", \n- "type": "txt"\n- }, \n- {\n- "name": "read_status", \n- "type": "tabular"\n- }, \n- {\n- "name": "trimmed_reads_fasta", \n- "type": "fasta"\n- }, \n- {\n- "name": "trimmed_reads_qual", \n- "type": "qual454"\n- }, \n- {\n- "name": "alignment_info", \n- "type": "tabular"\n- }, \n- {\n- "name": "all_contigs_fasta", \n- "type": "fasta"\n- }, \n- {\n- "name": "all_contigs_qual", \n- "type": "qual454"\n- }, \n- {\n- '..b'- "output_name": "outputfile"\n- }, \n- "inputTargetfile": {\n- "id": 6, \n- "output_name": "out_file1"\n- }, \n- "inputfastaFile": {\n- "id": 0, \n- "output_name": "output"\n- }\n- }, \n- "inputs": [\n- {\n- "description": "runtime parameter for tool Design primers to features", \n- "name": "min_size"\n- }, \n- {\n- "description": "runtime parameter for tool Design primers to features", \n- "name": "max_size"\n- }\n- ], \n- "name": "Design primers to features", \n- "outputs": [\n- {\n- "name": "primer_outputfile", \n- "type": "tabular"\n- }\n- ], \n- "position": {\n- "left": 1442.6968994140625, \n- "top": 314.98484802246094\n- }, \n- "post_job_actions": {}, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/Genetic_Marker_Design_2/1.0.0", \n- "tool_state": "{\\"__page__\\": 0, \\"inputTargetfile\\": \\"null\\", \\"inputfastaFile\\": \\"null\\", \\"min_size\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"inputSNPfile\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"max_size\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n- "tool_version": "1.0.0", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "8": {\n- "annotation": "Select successful design targets", \n- "id": 8, \n- "input_connections": {\n- "input": {\n- "id": 7, \n- "output_name": "primer_outputfile"\n- }\n- }, \n- "inputs": [], \n- "name": "Select", \n- "outputs": [\n- {\n- "name": "out_file1", \n- "type": "input"\n- }\n- ], \n- "position": {\n- "left": 1692.6968994140625, \n- "top": 316.92424011230469\n- }, \n- "post_job_actions": {}, \n- "tool_errors": null, \n- "tool_id": "Grep1", \n- "tool_state": "{\\"__page__\\": 0, \\"input\\": \\"null\\", \\"invert\\": \\"\\\\\\"true\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"pattern\\": \\"\\\\\\"NONE\\\\\\"\\"}", \n- "tool_version": "1.0.1", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "9": {\n- "annotation": "Remove duplicates", \n- "id": 9, \n- "input_connections": {\n- "inputFile": {\n- "id": 8, \n- "output_name": "out_file1"\n- }\n- }, \n- "inputs": [], \n- "name": "Unique", \n- "outputs": [\n- {\n- "name": "outputfile", \n- "type": "txt"\n- }\n- ], \n- "position": {\n- "left": 1900.6818237304688, \n- "top": 310.90907287597656\n- }, \n- "post_job_actions": {}, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/uni_Mask_1/1.0.0", \n- "tool_state": "{\\"__page__\\": 0, \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"inputFile\\": \\"null\\"}", \n- "tool_version": "1.0.0", \n- "type": "tool", \n- "user_outputs": []\n- }\n- }\n-}\n\\ No newline at end of file\n' |
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| diff -r be070a68521e -r b321e0517be3 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu May 22 20:30:19 2014 -0400 |
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| @@ -0,0 +1,24 @@ +galaxy-pcr-markers +================== + +Scripts for design of PCR-based Marker Assays from DNA sequence variant data, and xml wrappers for use in Galaxy workflow environment + +Also available for download at Galaxy Toolshed http://toolshed.g2.bx.psu.edu/ +hg clone http://toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers + +NOTE that the primer design tool *design_primers.py* relies on EMBOSS ePrimer3 which depends on Primer3 1.1.4. +The updated tool *design_HRM_primers.py* does not have this restriction and should work with Primer3 V2. + +Please see development branch HRM for optimised design of high-resolution melting PCR assays using the uMelt web service at University of Utah. + + +**CITATION** +A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: Application For Development Of A Framework Linkage Map In Bulb Onion (Allium cepa L.) (2012) + +Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum + +BMC Genomics 2012, 13:637 http://www.biomedcentral.com/1471-2164/13/637/abstract + +**Acknowledgements** +Current development of these tools is funded by the New Zealand Ministry for Business, Innovation & Employment project 'Virtual Institute of Statistical Genetics' (VISG) +See http://www.visg.co.nz |
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| diff -r be070a68521e -r b321e0517be3 design_primers.py --- a/design_primers.py Thu Oct 18 19:47:07 2012 -0400 +++ b/design_primers.py Thu May 22 20:30:19 2014 -0400 |
| [ |
| b'@@ -1,9 +1,13 @@\n-#!/usr/local/bin/python2.6\n-##design primers to features in multiple sequences\n-##usage: python design_primers.py <fasta-file> <gff file> <file of target IDs> <prod_min_size> <prod_max_size>\n \n+#!/usr/bin/env python\n+##design primers to features in multiple sequences, with option to predict melting\n+#usage: design_HRM_primers.py [-h] -i IN_FILE -g GFF_FILE -T TARGET_FILE [-u]\n+# [-n MAX_PRIMERS] [-p PROD_MIN_SIZE]\n+# [-P PROD_MAX_SIZE] [-l OPT_PRIMER_LENGTH]\n+# [-m MAX_TM_DIFF] [-t OPTIMUM_TM]\n+# [-G OPT_GC_PERCENT] [-x MAXPOLYX] [-c GC_CLAMP]\n \n-#Copyright 2012 John McCallum & Leshi Chen\n+#Copyright 2013 John McCallum & Susan Thomson\n #New Zealand Institute for Plant and Food Research\n #This program is free software: you can redistribute it and/or modify\n # it under the terms of the GNU General Public License as published by\n@@ -18,44 +22,86 @@\n # You should have received a copy of the GNU General Public License\n # along with this program. If not, see <http://www.gnu.org/licenses/>.\n \n-\n import os\n import StringIO\n import re\n-import tempfile\n-import subprocess\n import copy\n import sys\n from BCBio import GFF\n from BCBio.GFF import GFFExaminer\n from Bio import SeqIO\n-from Bio.Emboss.Applications import Primer3Commandline\n-from Bio.Emboss import Primer3\n+import run_p3 as P3\n+#import umelt_service as umelts\n+import argparse\t\n+\n+##Primer3 defaults or additional options defined as dictionary \n+def_dict={\n+\'PRIMER_MIN_SIZE\':\'18\',\n+\'PRIMER_MAX_SIZE\':\'25\',\n+\'PRIMER_MAX_NS_ACCEPTED\':\'1\'}\n+\n+#parse arguments\n+parser = argparse.ArgumentParser(description=\'Primer set design and melt prediction parameters\')\n+parser.add_argument(\'-i\', type=argparse.FileType(\'r\'), help="input sequence file, required", dest=\'in_file\', required=True)\n+parser.add_argument(\'-g\', type=argparse.FileType(\'r\'), help="input gff file with SNP and indels, required", dest=\'gff_file\', required=True)\n+parser.add_argument(\'-T\', type=argparse.FileType(\'r\'), help="input target SNP file, required", dest=\'target_file\', required=True)\n+parser.add_argument(\'-u\',help="do uMelt prediction, optional", dest=\'run_uMelt\',action=\'store_true\', default=False )\n+parser.add_argument(\'-n\', type=int, help="maximum number of primer pairs to return, default=5", dest=\'max_primers\', default=5) ## PRIMER_NUM_RETURN\n+parser.add_argument(\'-p\', type=int, help="minimum product size", dest=\'prod_min_size\', default=100) ## PRIMER_PRODUCT_SIZE_RANGE min\n+parser.add_argument(\'-P\', type=int, help="maximum product size", dest=\'prod_max_size\', default=300) ## PRIMER_PRODUCT_SIZE_RANGE max\n+parser.add_argument(\'-l\', type=int, help="optimum primer length", dest=\'opt_primer_length\', default=20) ## PRIMER_OPT_SIZE\n+parser.add_argument(\'-m\', type=int, help="maximum tm difference between primers", dest=\'max_tm_diff\', default=1) ## PRIMER_PAIR_MAX_DIFF_TM\n+parser.add_argument(\'-t\', type=int, help="optimum Tm for primers, recommend range 59 to 61", dest=\'optimum_tm\', default=59) ## PRIMER_OPT_TM\n+parser.add_argument(\'-G\', type=int, help="optimum GC percentage of primers", dest=\'opt_GC_percent\', default=50) ## PRIMER_OPT_GC_PERCENT\n+parser.add_argument(\'-x\', type=int, help="maximum polyx, recommend less than 4", dest=\'maxpolyx\', default=3) ## PRIMER_MAX_POLY_X\n+parser.add_argument(\'-c\', type=int, help="number of C/Gs at end, recommend 2", dest=\'gc_clamp\', default=1) ## PRIMER_GC_CLAMP\n+\n+parser.add_argument(\'-e\', type=int, help="maximum allowable 3\'-anchored complementarity", dest=\'maxselfend\', default=3) ## PRIMER_MAX_SELF_END\n+parser.add_argument(\'-a\', type=int, help="maximum complementarity between left and right or self", dest=\'maxselfany\', default=8) ## PRIMER_MAX_SELF_ANY\n+parser.add_a'..b'", p3_exclude_str)\n- #add temporary output file to get the result\n- primer_cl.set_parameter("-outfile", tempproutfile)\n- #specify maximum different of tm\n- primer_cl.set_parameter("-maxdifftm",max_tm_diff )\n- #other useful parameters\n- primer_cl.set_parameter("-ogcpercent", opt_GC_percent)\n- primer_cl.set_parameter("-opolyxmax", maxpolyx) \n- primer_cl.set_parameter("-osize", optimum_length)\n- #set product size range\n- primer_cl.set_parameter("-prange", productsizerange)\n- #using python subprocess method to run emboss command line programe with the parameters given\n- fnull = open(os.devnull, \'w\')\n- result=subprocess.check_call(str(primer_cl),shell=True ,stdout = fnull, stderr = fnull)\n- #read temporary outputfile\n- handle = open(tempproutfile)\n- record = Primer3.read(handle)\n- ##just return first set, if there is one\n- if len(record.primers) > 0:\n- primer= record.primers[0]\n- outputstr=[mytarget.id, primer.forward_seq,primer.reverse_seq,primer.size]\n- else:\n- outputstr=[mytarget.id,"NONE","NONE","NONE"]\n- print(\'\\t\'.join(map(str,outputstr)))\n+\t\t\texcludes_str=\' \'.join([str(x.location.start.position)+\',\'+str(x.location.end.position -x.location.start.position) for x in exclude_feat])\n+ my_target_dict={\'SEQUENCE_ID\' : rec.name, \'SEQUENCE_TEMPLATE\': targetRec.seq.tostring(),\'SEQUENCE_TARGET\': str(target_feat.location.start.position) + \',1\',\'SEQUENCE_INTERNAL_EXCLUDED_REGION\': excludes_str}\n+ my_target_dict.update(def_dict) ##add in defaults\n+\t\t\tresult=P3.run_P3(target_dict=my_target_dict)\n+ if my_args.run_uMelt:\n+ amp_seq=targetRec.seq ##need to make this conditional on getting a result >0 and melt=True\n+ mutamp_seq=targetRec.seq.tomutable()\n+ mutamp_seq[target_feat.location.start:target_feat.location.end]=target_feat.qualifiers[\'Variant_seq\'][0] #mutate to variant\n+\t\t\tfor primerset in result:\n+\t\t\t\tamp_start=int(primerset[\'PRIMER_LEFT\'].split(\',\')[0])\n+\t\t\t\tamp_end=int(primerset[\'PRIMER_RIGHT\'].split(\',\')[0])\n+ ref_melt_Tm=0\n+ var_melt_Tm=0\n+ if my_args.run_uMelt:\n+ try:\n+ ref_melt_Tm=umelts.getTm(umelts.getmelt(amp_seq.tostring()[amp_start:amp_end+1]))\n+\t\t\t\t\tvar_melt_Tm=umelts.getTm(umelts.getmelt(mutamp_seq.tostring()[amp_start:amp_end+1]))\n+ except:\n+\t\t\t\t\tref_melt_Tm=0 ##preferably something more informative?\n+\t\t\t\t\tvar_melt_Tm=0 ##exception handling to be added\n+ reference_seq=target_feat.qualifiers[\'Reference_seq\'][0]\n+ if target_feat.qualifiers.has_key(\'Variant_seq\'):\n+ variant_seq=target_feat.qualifiers[\'Variant_seq\'][0]\n+ else:\n+ variant_seq="NA"\n+ print mytarget.id, featLocation + 1 ,reference_seq, variant_seq,amp_end-amp_start,primerset[\'PRIMER_LEFT_SEQUENCE\'],primerset[\'PRIMER_RIGHT_SEQUENCE\'], ref_melt_Tm,var_melt_Tm,abs(ref_melt_Tm-var_melt_Tm)#, amp_seq.tostring()[amp_start:amp_end+1], mutamp_seq.tostring()[amp_start:amp_end+1]\n \n- \n-in_gff_handle.close()\n-in_seq_handle.close()\n+my_args.gff_file.close()\n+my_args.in_file.close()\n+\n' |
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| diff -r be070a68521e -r b321e0517be3 design_primers.xml --- a/design_primers.xml Thu Oct 18 19:47:07 2012 -0400 +++ b/design_primers.xml Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -1,14 +1,25 @@ <?xml version="1.0"?> <tool id="Genetic_Marker_Design_2" name="Design primers to features"> <description>Design PCR Primers to Features</description> - <command interpreter="python">design_primers.py $inputfastaFile $inputSNPfile $inputTargetfile $min_size $max_size > $primer_outputfile </command> + <command interpreter="python -W ignore"> + #if 'Yes' in $uMelt.value + design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size -u > $primer_outputfile + #else + design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size > $primer_outputfile + #end if + </command> + <inputs> <param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" /> <param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" /> <param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="IN FORMAT Sequence id:source:type:start e.g. 1174806:gsMapper:SNP:292" ></param> <param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" /> <param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" /> - </inputs> + <param name="uMelt" type="select" label="uMelt prediction for HRM"> + <option value="No" selected= "true">No</option> + <option value="Yes">Yes</option> + </param> + </inputs> <outputs> <data format="tabular" name="primer_outputfile" /> </outputs> @@ -18,6 +29,7 @@ **TIP** This tool designs primer pairs to flank features +Optionally it can predict reference and variant Tm using the uMelt web service provided by University of Utah It takes |
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| diff -r be070a68521e -r b321e0517be3 find_CAPS.xml --- a/find_CAPS.xml Thu Oct 18 19:47:07 2012 -0400 +++ b/find_CAPS.xml Thu May 22 20:30:19 2014 -0400 |
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| @@ -9,6 +9,13 @@ <outputs> <data format="interval" name="outputfile" /> </outputs> + <tests> + <test> + <param name="inputSNPGff3File" value="targets.gff" ftype="gff3"/> + <param name="inputFasta" value="targets.fasta" ftype="fasta"/> + <output name="outputfile" file="find_caps_output.txt"/> + </test> + </tests> <help> .. class:: infomark @@ -32,7 +39,7 @@ -*input GFF* +*input GFF3* :: |
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| diff -r be070a68521e -r b321e0517be3 gsmapper2gff.sh --- a/gsmapper2gff.sh Thu Oct 18 19:47:07 2012 -0400 +++ b/gsmapper2gff.sh Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -15,6 +15,8 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. +##usage gsmapper2gff.sh <input 454HCDiffs.txt or 454AllDiffs.txt file> <output gff3 file> + infile=$1 outfile=$2 |
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| diff -r be070a68521e -r b321e0517be3 ipcress.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipcress.xml Thu May 22 20:30:19 2014 -0400 |
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| @@ -0,0 +1,56 @@ +<?xml version="1.0"?> +<tool id="ipcress" name="In-Silico PCR Experiment Simulation System"> + <description>In-Silico PCR Experiment Simulation System</description> + <version_command>ipcress -v</version_command> + <command> + awk -v min=$min_length -v max=$max_length '{print $1,$2,$3, min, max}' $input_primers | ipcress -i /dev/stdin -s $input_seqs -m $mismatch $products_as_fasta $pretty -S $seed_length > $pcr_products + </command> + <inputs> + <param format="txt" name="input_primers" type="data" label="PCR Experiment Data" /> + <param format="fasta" name="input_seqs" type="data" label="Sequences (Fasta)" /> + <param name="mismatch" size="10" type="integer" value="0" label="Mismatches allowed per primer" /> + <param name="min_length" size="10" type="integer" value="50" label="Minimum PCR product length" /> + <param name="max_length" size="10" type="integer" value="100" label="Maximum PCR product length" /> + <param name="products_as_fasta" type="boolean" truevalue="-P" falsevalue="" label="Display PCR products as a FASTA format sequence" /> + <param name="pretty" type="boolean" truevalue="-p 1" falsevalue="-p 0" checked="true" label="Display Result in pretty format" /> + <param name="seed_length" size="10" type="integer" value="12" label="Seed length: 0 => Use Full Primer Length" /> + </inputs> + <outputs> + <data format="txt" name="pcr_products" /> + </outputs> + <stdio> + <exit_code range="1:" level="fatal" description="Fatal Error" /> + </stdio> + <tests> + <test> + <param name="input_primers" value="ipcress_test_input.txt" ftype="txt" /> + <param name="input_seqs" value="targets.fasta" ftype="fasta" /> + <output name="pcr_products" file="ipcress.out" /> + </test> + </tests> + <help> +ipcress is the In-silico PCR Experiment Simulation System. + +This is a tool for simulation of PCR experiments. You supply a file containing primers and a set of sequences, and it predicts PCR products. + +INPUT FORMAT + +The input for ipcress is a simple white-space delimited file describing +one experiment per line. Each line contains the following 5 fields: + +id An identifier for this experiment +primer_A Sequence for the first primer +primer_B Sequence for the second primer +min_product_len Minimum product length to report +max_product_len Maximum product length to report + +Here is an example line in this format: + +ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100 + +MANUAL + +https://www.ebi.ac.uk/~guy/exonerate/ipcress.man.html + + </help> +</tool> |
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| diff -r be070a68521e -r b321e0517be3 ipcress_gff.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipcress_gff.xml Thu May 22 20:30:19 2014 -0400 |
| [ |
| @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool id="ipcress_gff" name="IPCRESS to GFF"> + <description>Convert output from In-Silico PCR Experiment Simulation System to GFF format</description> + <command> + awk '/^ipcress:/, split($2,HIT,":"){print HIT[1],$3,$4,$5,$6,$7,$8,$9,$10,$11}' $input1 | awk -v OFS='\t' '{print $1,"ipcress","PCR_product",$5,$8,".","+",".","Name="$2}' > $output1 + </command> + <inputs> + <param format="txt" name="input1" type="data" label="iPCRESS ouptut" /> + </inputs> + <outputs> + <data format="gff" name="output1" /> + </outputs> + <tests> + <test> + <param name="input1" value="ipcress.out" ftype="txt" /> + <output name="output1" file="ipcress_gff.out" /> + </test> + </tests> + <help> +Uses awk to parse IPCRESS output to gff file format + </help> +</tool> |
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| diff -r be070a68521e -r b321e0517be3 parse_primersearch.pl --- a/parse_primersearch.pl Thu Oct 18 19:47:07 2012 -0400 +++ b/parse_primersearch.pl Thu May 22 20:30:19 2014 -0400 |
| [ |
| @@ -1,7 +1,7 @@ #!/usr/bin/perl #parse_primersearch.pl #reformat EMBOSS primersearch output into columnar Galaxy interval format - +#usage perl parse_primersearch.pl <input primersearch file> <tabular output file> #Copyright 2012 John McCallum #New Zealand Institute for Plant and Food Research #This program is free software: you can redistribute it and/or modify @@ -20,7 +20,7 @@ open (IN, "<$ARGV[0]"); open (OUT, ">$ARGV[1]"); -#print OUT "primerset_id","\t","sequence_id","\t","hit_start","\","mismatches","\t","amplimer_size",\n"; + |
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| diff -r be070a68521e -r b321e0517be3 run_p3.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_p3.py Thu May 22 20:30:19 2014 -0400 |
| [ |
| @@ -0,0 +1,49 @@ +#!/usr/bin/pyrthon +##run primer3 by passing Python dictionary + +#un_P3.py + +import subprocess as sp +import copy + + +if "check_output" not in dir(sp): # duck punch it in! + def f(*popenargs, **kwargs): + if 'stdout' in kwargs: + raise ValueError('stdout argument not allowed, it will be overridden.') + process = sp.Popen(stdout=sp.PIPE, *popenargs, **kwargs) + output, unused_err = process.communicate() + retcode = process.poll() + if retcode: + cmd = kwargs.get("args") + if cmd is None: + cmd = popenargs[0] + raise sp.CalledProcessError(retcode,cmd) + return output + sp.check_output = f + + + + +##call P3 with dict of args, returns dict, no exception handling +def run_P3(target_dict): + p3_str='' + for key in target_dict: + p3_str+=key + p3_str+='=' + p3_str+=str(target_dict[key]) + p3_str+='\n' + p3_str+='=' + input_str='echo -e \"' + p3_str + '\" | primer3_core ' +###exception handling to be added here + output = sp.check_output(input_str,shell=True) + output_fields=output.split('\n') + ##put output into a dict, omitting trailing = + P3_dict=dict([X.split('=') for X in output_fields][:len(output_fields)-2]) + ##return iterable list + primer_list=[dict(PRIMER_RIGHT_SEQUENCE=P3_dict.get('PRIMER_RIGHT_'+ str(X) + '_SEQUENCE'),PRIMER_LEFT=P3_dict.get('PRIMER_LEFT_'+ str(X) ),PRIMER_RIGHT=P3_dict.get('PRIMER_RIGHT_'+ str(X) ),PRIMER_LEFT_SEQUENCE=P3_dict.get('PRIMER_LEFT_'+ str(X) + '_SEQUENCE')) for X in range(0,int(P3_dict.get('PRIMER_RIGHT_NUM_RETURNED'))-1)] + return(primer_list) + + + + |
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| diff -r be070a68521e -r b321e0517be3 test-data/find_caps_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_caps_output.txt Thu May 22 20:30:19 2014 -0400 |
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| @@ -0,0 +1,1 @@ +k69_93535 1147 1149 k69_93535:SAMTOOLS:SNP:1147 TaqI variant |
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| diff -r be070a68521e -r b321e0517be3 test-data/freebayes_out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes_out.vcf Thu May 22 20:30:19 2014 -0400 |
| b |
| b'@@ -0,0 +1,500 @@\n+##fileformat=VCFv4.1\n+##fileDate=20140410\n+##source=freeBayes version 0.9.6\n+##reference=localref.fa\n+##phasing=none\n+##commandline="freebayes --bam localbam_0.bam --fasta-reference localref.fa --vcf /data/galaxy/galaxy-dist/database/files/000/dataset_31.dat"\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">\n+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observations">\n+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations">\n+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">\n+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">\n+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">\n+##INFO=<ID=XRM,Number=1,Type=Float,Description="Reference allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads supporting the reference allele.">\n+##INFO=<ID=XRS,Number=1,Type=Float,Description="Reference allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in reads supporting the reference allele.">\n+##INFO=<ID=XRI,Number=1,Type=Float,Description="Reference allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the reference allele.">\n+##INFO=<ID=XAM,Number=A,Type=Float,Description="Alternate allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads supporting the alternate allele, excluding the called variant.">\n+##INFO=<ID=XAS,Number=A,Type=Float,Descriptio'..b'.50735\t.\tAB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01\tGT:GQ:DP:RO:QR:AO:QA:GL\t0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23\n+Chr1\t62665\t.\tG\tC\t2.50735\t.\tAB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01\tGT:GQ:DP:RO:QR:AO:QA:GL\t0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23\n+Chr1\t62686\t.\tA\tT\t4.77465\t.\tAB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7\n+Chr1\t62697\t.\tC\tA\t4.77465\t.\tAB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7\n+Chr1\t62758\t.\tG\tT\t17.1701\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0\n+Chr1\t62769\t.\tA\tC\t17.1701\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0\n+Chr1\t62841\t.\tT\tG\t17.1701\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0\n+Chr1\t62852\t.\tC\tG\t17.1701\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0\n+Chr1\t62929\t.\tC\tA\t17.1701\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0\n+Chr1\t63049\t.\tA\tT\t17.1701\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0\n+Chr1\t63120\t.\tC\tA\t4.77465\t.\tAB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR\tGT:GQ:DP:RO:QR:AO:QA:GL\t0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7\n' |
| b |
| diff -r be070a68521e -r b321e0517be3 test-data/freebayes_vcf_to_gff_output.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes_vcf_to_gff_output.gff Thu May 22 20:30:19 2014 -0400 |
| b |
| b'@@ -0,0 +1,449 @@\n+#gff-version 3\n+Chr1\tSAMTOOLS\tSNP\t106\t106\t17.1701\t.\t.\tID=Chr1:SNP:106;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t200\t200\t17.1701\t.\t.\tID=Chr1:SNP:200;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t217\t217\t4.77465\t.\t.\tID=Chr1:SNP:217;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t249\t249\t4.77465\t.\t.\tID=Chr1:SNP:249;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t586\t586\t17.1701\t.\t.\tID=Chr1:SNP:586;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t669\t669\t4.77465\t.\t.\tID=Chr1:SNP:669;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t682\t682\t4.77465\t.\t.\tID=Chr1:SNP:682;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t1007\t1007\t17.1701\t.\t.\tID=Chr1:SNP:1007;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1012\t1012\t17.1701\t.\t.\tID=Chr1:SNP:1012;Variant_seq=AGA;Reference_seq=TGT;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1056\t1056\t17.1701\t.\t.\tID=Chr1:SNP:1056;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1067\t1067\t17.1701\t.\t.\tID=Chr1:SNP:1067;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1257\t1257\t17.1701\t.\t.\tID=Chr1:SNP:1257;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1305\t1305\t17.1701\t.\t.\tID=Chr1:SNP:1305;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1319\t1319\t17.1701\t.\t.\tID=Chr1:SNP:1319;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1330\t1330\t17.1701\t.\t.\tID=Chr1:SNP:1330;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1441\t1441\t17.1701\t.\t.\tID=Chr1:SNP:1441;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1451\t1451\t17.1701\t.\t.\tID=Chr1:SNP:1451;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1460\t1460\t17.1701\t.\t.\tID=Chr1:SNP:1460;Variant_seq=ATCTC;Reference_seq=CTCTG;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1480\t1480\t17.1701\t.\t.\tID=Chr1:SNP:1480;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1525\t1525\t17.1701\t.\t.\tID=Chr1:SNP:1525;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t1670\t1670\t4.77465\t.\t.\tID=Chr1:SNP:1670;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t1673\t1673\t4.77465\t.\t.\tID=Chr1:SNP:1673;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t1700\t1700\t4.77465\t.\t.\tID=Chr1:SNP:1700;Variant_seq=TG;Reference_seq=GC;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t1711\t1711\t4.77465\t.\t.\tID=Chr1:SNP:1711;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t2117\t2117\t17.1701\t.\t.\tID=Chr1:SNP:2117;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t2154\t2154\t17.1701\t.\t.\tID=Chr1:SNP:2154;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t2485\t2485\t17.1701\t.\t.\tID=Chr1:SNP:2485;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t2490\t2490\t17.1701\t.\t.\tID=Chr1:SNP:2490;Variant_seq=CAC;Reference_seq=AAA;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t2906\t2906\t17.1701\t.\t.\tID=Chr1:SNP:2906;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t2925\t2925\t17.1701\t.\t.\tID=Chr1:SNP:2925;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t3371\t3371\t17.1701\t.\t.\tID=Chr1:SNP:3371;Variant_seq=GCCTA;Reference_seq=CCCTT;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t3389\t3389\t17.1701\t.\t.\tID=Chr1:SNP:3389;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t3431\t3431\t17.1701\t.\t.\tID=Chr1:SNP:3431;Variant_seq=T;Reference_seq=G;'..b'reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t59546\t59546\t17.1701\t.\t.\tID=Chr1:SNP:59546;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t59554\t59554\t46.0861\t.\t.\tID=Chr1:SNP:59554;Variant_seq=CG;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t61378\t61378\t17.1701\t.\t.\tID=Chr1:SNP:61378;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t61387\t61387\t17.1701\t.\t.\tID=Chr1:SNP:61387;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t61599\t61599\t17.1701\t.\t.\tID=Chr1:SNP:61599;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t61652\t61652\t17.1701\t.\t.\tID=Chr1:SNP:61652;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t61882\t61882\t17.1701\t.\t.\tID=Chr1:SNP:61882;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t61904\t61904\t17.1701\t.\t.\tID=Chr1:SNP:61904;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t61913\t61913\t17.1701\t.\t.\tID=Chr1:SNP:61913;Variant_seq=TGC;Reference_seq=AGG;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t61957\t61957\t17.1701\t.\t.\tID=Chr1:SNP:61957;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62010\t62010\t17.1701\t.\t.\tID=Chr1:SNP:62010;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62056\t62056\t4.77465\t.\t.\tID=Chr1:SNP:62056;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t62168\t62168\t17.1701\t.\t.\tID=Chr1:SNP:62168;Variant_seq=GCGCG;Reference_seq=CCGCC;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62290\t62290\t17.1701\t.\t.\tID=Chr1:SNP:62290;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62446\t62446\t2.50735\t.\t.\tID=Chr1:SNP:62446;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET \n+Chr1\tSAMTOOLS\tSNP\t62447\t62447\t2.50735\t.\t.\tID=Chr1:SNP:62447;Variant_seq=ATAC;Reference_seq=CTAG;Total_reads=3;Zygosity=3:HET \n+Chr1\tSAMTOOLS\tSNP\t62462\t62462\t2.50735\t.\t.\tID=Chr1:SNP:62462;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET \n+Chr1\tSAMTOOLS\tSNP\t62478\t62478\t2.50735\t.\t.\tID=Chr1:SNP:62478;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET \n+Chr1\tSAMTOOLS\tSNP\t62514\t62514\t4.77465\t.\t.\tID=Chr1:SNP:62514;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t62598\t62598\t17.1701\t.\t.\tID=Chr1:SNP:62598;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62634\t62634\t4.77465\t.\t.\tID=Chr1:SNP:62634;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t62658\t62658\t2.50735\t.\t.\tID=Chr1:SNP:62658;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET \n+Chr1\tSAMTOOLS\tSNP\t62665\t62665\t2.50735\t.\t.\tID=Chr1:SNP:62665;Variant_seq=C;Reference_seq=G;Total_reads=3;Zygosity=3:HET \n+Chr1\tSAMTOOLS\tSNP\t62686\t62686\t4.77465\t.\t.\tID=Chr1:SNP:62686;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t62697\t62697\t4.77465\t.\t.\tID=Chr1:SNP:62697;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET \n+Chr1\tSAMTOOLS\tSNP\t62758\t62758\t17.1701\t.\t.\tID=Chr1:SNP:62758;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62769\t62769\t17.1701\t.\t.\tID=Chr1:SNP:62769;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62841\t62841\t17.1701\t.\t.\tID=Chr1:SNP:62841;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62852\t62852\t17.1701\t.\t.\tID=Chr1:SNP:62852;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t62929\t62929\t17.1701\t.\t.\tID=Chr1:SNP:62929;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t63049\t63049\t17.1701\t.\t.\tID=Chr1:SNP:63049;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut \n+Chr1\tSAMTOOLS\tSNP\t63120\t63120\t4.77465\t.\t.\tID=Chr1:SNP:63120;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET \n' |
| b |
| diff -r be070a68521e -r b321e0517be3 test-data/ipcress.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ipcress.out Thu May 22 20:30:19 2014 -0400 |
| b |
| b"@@ -0,0 +1,341 @@\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_93535:SAMTOOLS:SNP:1147\n+ Primers: A B\n+ Target: k69_93535:filter(unmasked)\n+ Matches: 20/20 23/23\n+ Product: 83 bp (range 50-100)\n+Result type: forward\n+\n+...GGACAGGGAAGCTTCATAGG................................. # forward\n+ ||||||||||||||||||||-->\n+5'-GGACAGGGAAGCTTCATAGG-3' 3'-CTCCTAAACTAGAAAGTCCAAAC-5' # primers\n+ <--|||||||||||||||||||||||\n+..............................CTCCTAAACTAGAAAGTCCAAAC... # revcomp\n+--\n+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 83 A 1088 0 B 1148 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_93535:SAMTOOLS:SNP:1147\n+ Primers: A B\n+ Target: k69_93535:filter(unmasked)\n+ Matches: 21/21 21/21\n+ Product: 86 bp (range 50-100)\n+Result type: forward\n+\n+...CTTTGAGTCTGAACGCATTTG............................... # forward\n+ |||||||||||||||||||||-->\n+5'-CTTTGAGTCTGAACGCATTTG-3' 3'-CTTCTTTGCCCTCTACTTTGT-5' # primers\n+ <--|||||||||||||||||||||\n+...............................CTTCTTTGCCCTCTACTTTGT... # revcomp\n+--\n+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 86 A 1109 0 B 1174 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_93535:SAMTOOLS:SNP:1147\n+ Primers: A B\n+ Target: k69_93535:filter(unmasked)\n+ Matches: 20/20 20/20\n+ Product: 87 bp (range 50-100)\n+Result type: forward\n+\n+...TTTGAGTCTGAACGCATTTG.............................. # forward\n+ ||||||||||||||||||||-->\n+5'-TTTGAGTCTGAACGCATTTG-3' 3'-CTTTGCCCTCTACTTTGTTC-5' # primers\n+ <--||||||||||||||||||||\n+..............................CTTTGCCCTCTACTTTGTTC... # revcomp\n+--\n+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 87 A 1110 0 B 1177 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_93535:SAMTOOLS:SNP:1147\n+ Primers: A B\n+ Target: k69_93535:filter(unmasked)\n+ Matches: 21/21 21/21\n+ Product: 89 bp (range 50-100)\n+Result type: forward\n+\n+...CTTTGAGTCTGAACGCATTTG............................... # forward\n+ |||||||||||||||||||||-->\n+5'-CTTTGAGTCTGAACGCATTTG-3' 3'-CTTTGCCCTCTACTTTGTTCT-5' # primers\n+ <--|||||||||||||||||||||\n+...............................CTTTGCCCTCTACTTTGTTCT... # revcomp\n+--\n+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 89 A 1109 0 B 1177 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_93535:SAMTOOLS:SNP:1147\n+ Primers: A B\n+ Target: k69_93535:filter(unmasked)\n+ Matches: 21/21 21/21\n+ Product: 93 bp (range 50-100)\n+Result type: forward\n+\n+...CTTTGAGTCTGAACGCATTTG............................... # forward\n+ |||||||||||||||||||||-->\n+5'-CTTTGAGTCTGAACGCATTTG-3' 3'-GCCCTCTACTTTGTTCTAAAC-5' # primers\n+ <--|||||||||||||||||||||\n+...............................GCCCTCTACTTTGTTCTAAAC... # revcomp\n+--\n+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 93 A 1109 0 B 1181 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_93535:SAMTOOLS:SNP:1336\n+ Primers: A B\n+ Target: k69_93535:filter(unmasked)\n+ Matches: 20/20 22/22\n+ Product: 82 bp (range 50-100)\n+Result type: forward\n+\n+...TTAGAAGGAACGCGAGAAGG................................ # forward\n+ ||||||||||||||||||||-->\n+5'-TTAGAAGGAACGCGAGAAGG-3' 3'-GAATGCGGATCAAACCAACAAC-5' # primers\n+ <--||||||||||||||||||||||\n+..............................GAATGCGGATCAAACCAACAAC... # revcomp\n+--\n+ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 82 A 1297 0 B 1357 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_93535:SAMTOOLS:SNP:1336\n+ Primers: A B\n+ Target: k69_93535:filter(unmasked)\n+ Matches: 20/20 20/20\n+ Product: 85 bp (range 50-100)\n+Result type: forward\n+\n+...TTTAGAAGGAACGCGAGAAG.............................. # forward\n+ ||||||||||||||||||||-->\n+5'-TTTAGAAGGAACGCGAGAAG-3' 3'-GCGGATCAAACCAACAACAA-5' # primer"..b"+5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-GCAGTCTAGTAGTTGTGCTT-5' # primers\n+ <--||||||||||||||||||||\n+...................................GCAGTCTAGTAGTTGTGCTT... # revcomp\n+--\n+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 96 A 1 0 B 77 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_98089:SAMTOOLS:SNP:30\n+ Primers: A B\n+ Target: k69_98089:filter(unmasked)\n+ Matches: 25/25 21/21\n+ Product: 97 bp (range 50-100)\n+Result type: forward\n+\n+...CAAATCCAAACATGTTATCTTCTTC............................... # forward\n+ |||||||||||||||||||||||||-->\n+5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-GCAGTCTAGTAGTTGTGCTTG-5' # primers\n+ <--|||||||||||||||||||||\n+...................................GCAGTCTAGTAGTTGTGCTTG... # revcomp\n+--\n+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 97 A 1 0 B 77 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_98089:SAMTOOLS:SNP:550\n+ Primers: A B\n+ Target: k69_98089:filter(unmasked)\n+ Matches: 22/22 24/24\n+ Product: 88 bp (range 50-100)\n+Result type: forward\n+\n+...TGAATTGATACTGAAATTCGGG.................................. # forward\n+ ||||||||||||||||||||||-->\n+5'-TGAATTGATACTGAAATTCGGG-3' 3'-CTAACACCTTTGAAAGTACATACG-5' # primers\n+ <--||||||||||||||||||||||||\n+................................CTAACACCTTTGAAAGTACATACG... # revcomp\n+--\n+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 88 A 499 0 B 563 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_98089:SAMTOOLS:SNP:550\n+ Primers: A B\n+ Target: k69_98089:filter(unmasked)\n+ Matches: 22/22 24/24\n+ Product: 77 bp (range 50-100)\n+Result type: forward\n+\n+...TGAAATTCGGGAAGACTGAAAG.................................. # forward\n+ ||||||||||||||||||||||-->\n+5'-TGAAATTCGGGAAGACTGAAAG-3' 3'-CTAACACCTTTGAAAGTACATACG-5' # primers\n+ <--||||||||||||||||||||||||\n+................................CTAACACCTTTGAAAGTACATACG... # revcomp\n+--\n+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 77 A 510 0 B 563 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_98089:SAMTOOLS:SNP:550\n+ Primers: A B\n+ Target: k69_98089:filter(unmasked)\n+ Matches: 19/19 25/25\n+ Product: 75 bp (range 50-100)\n+Result type: forward\n+\n+...CGGGAAGACTGAAAGAACG................................... # forward\n+ |||||||||||||||||||-->\n+5'-CGGGAAGACTGAAAGAACG-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers\n+ <--|||||||||||||||||||||||||\n+.............................CACCTTTGAAAGTACATACGATAGA... # revcomp\n+--\n+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 75 A 517 0 B 567 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_98089:SAMTOOLS:SNP:550\n+ Primers: A B\n+ Target: k69_98089:filter(unmasked)\n+ Matches: 21/21 25/25\n+ Product: 81 bp (range 50-100)\n+Result type: forward\n+\n+...GAAATTCGGGAAGACTGAAAG................................... # forward\n+ |||||||||||||||||||||-->\n+5'-GAAATTCGGGAAGACTGAAAG-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers\n+ <--|||||||||||||||||||||||||\n+...............................CACCTTTGAAAGTACATACGATAGA... # revcomp\n+--\n+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 81 A 511 0 B 567 0 forward\n+\n+Ipcress result\n+--------------\n+ Experiment: k69_98089:SAMTOOLS:SNP:550\n+ Primers: A B\n+ Target: k69_98089:filter(unmasked)\n+ Matches: 22/22 25/25\n+ Product: 79 bp (range 50-100)\n+Result type: forward\n+\n+...AATTCGGGAAGACTGAAAGAAC................................... # forward\n+ ||||||||||||||||||||||-->\n+5'-AATTCGGGAAGACTGAAAGAAC-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers\n+ <--|||||||||||||||||||||||||\n+................................CACCTTTGAAAGTACATACGATAGA... # revcomp\n+--\n+ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 79 A 513 0 B 567 0 forward\n+-- completed ipcress analysis\n" |
| b |
| diff -r be070a68521e -r b321e0517be3 test-data/ipcress_gff.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ipcress_gff.out Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -0,0 +1,20 @@ +k69_93535 ipcress PCR_product 1088 1148 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1109 1174 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1110 1177 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1109 1177 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1109 1181 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1297 1357 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_93535 ipcress PCR_product 1296 1361 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_93535 ipcress PCR_product 1295 1361 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_93535 ipcress PCR_product 1297 1362 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_93535 ipcress PCR_product 1297 1363 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_98089 ipcress PCR_product 1 70 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 1 71 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 1 71 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 1 77 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 1 77 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 499 563 . + . Name=k69_98089:SAMTOOLS:SNP:550 +k69_98089 ipcress PCR_product 510 563 . + . Name=k69_98089:SAMTOOLS:SNP:550 +k69_98089 ipcress PCR_product 517 567 . + . Name=k69_98089:SAMTOOLS:SNP:550 +k69_98089 ipcress PCR_product 511 567 . + . Name=k69_98089:SAMTOOLS:SNP:550 +k69_98089 ipcress PCR_product 513 567 . + . Name=k69_98089:SAMTOOLS:SNP:550 |
| b |
| diff -r be070a68521e -r b321e0517be3 test-data/ipcress_test_input.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ipcress_test_input.txt Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -0,0 +1,20 @@ +k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG TGTTTCATCTCCCGTTTCTTC +k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG TCTTGTTTCATCTCCCGTTTC +k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG CAAATCTTGTTTCATCTCCCG +k69_93535:SAMTOOLS:SNP:1147 TTTGAGTCTGAACGCATTTG CTTGTTTCATCTCCCGTTTC +k69_93535:SAMTOOLS:SNP:1147 GGACAGGGAAGCTTCATAGG CAAACCTGAAAGATCAAATCCTC +k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG CAACAACCAAACTAGGCGTAAG +k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG CTCAACAACAACCAAACTAGGC +k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG GCTCAACAACAACCAAACTAGG +k69_93535:SAMTOOLS:SNP:1336 TTTAGAAGGAACGCGAGAAG AACAACAACCAAACTAGGCG +k69_93535:SAMTOOLS:SNP:1336 GTTTAGAAGGAACGCGAGAAG AACAACAACCAAACTAGGCG +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC TTCGTGTTGATGATCTGACG +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GTTCGTGTTGATGATCTGACG +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC TTGATGATCTGACGTTGAGC +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GTTGATGATCTGACGTTGAGC +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GATGATCTGACGTTGAGCG +k69_98089:SAMTOOLS:SNP:550 TGAATTGATACTGAAATTCGGG GCATACATGAAAGTTTCCACAATC +k69_98089:SAMTOOLS:SNP:550 CGGGAAGACTGAAAGAACG AGATAGCATACATGAAAGTTTCCAC +k69_98089:SAMTOOLS:SNP:550 GAAATTCGGGAAGACTGAAAG AGATAGCATACATGAAAGTTTCCAC +k69_98089:SAMTOOLS:SNP:550 AATTCGGGAAGACTGAAAGAAC AGATAGCATACATGAAAGTTTCCAC +k69_98089:SAMTOOLS:SNP:550 TGAAATTCGGGAAGACTGAAAG GCATACATGAAAGTTTCCACAATC |
| b |
| diff -r be070a68521e -r b321e0517be3 test-data/mpileup_out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup_out.vcf Thu May 22 20:30:19 2014 -0400 |
| b |
| b'@@ -0,0 +1,500 @@\n+##fileformat=VCFv4.1\n+##samtoolsVersion=0.1.19-44428cd\n+##reference=file:///tmp/tmp-SAMTOOLS-zkHTpr/reference_input.fa\n+##contig=<ID=Chr1,length=17971566>\n+##contig=<ID=Chr10,length=15490421>\n+##contig=<ID=Chr11,length=17082262>\n+##contig=<ID=Chr12,length=13002763>\n+##contig=<ID=Chr13,length=17372821>\n+##contig=<ID=Chr14,length=12031045>\n+##contig=<ID=Chr15,length=19001909>\n+##contig=<ID=Chr16,length=11476499>\n+##contig=<ID=Chr17,length=14675105>\n+##contig=<ID=Chr18,length=14814751>\n+##contig=<ID=Chr19,length=11145676>\n+##contig=<ID=Chr2,length=15003700>\n+##contig=<ID=Chr20,length=14375345>\n+##contig=<ID=Chr21,length=14287830>\n+##contig=<ID=Chr22,length=12982530>\n+##contig=<ID=Chr23,length=20688064>\n+##contig=<ID=Chr24,length=17702303>\n+##contig=<ID=Chr25,length=14321294>\n+##contig=<ID=Chr26,length=17153587>\n+##contig=<ID=Chr27,length=10917718>\n+##contig=<ID=Chr28,length=16406049>\n+##contig=<ID=Chr29,length=14180785>\n+##contig=<ID=Chr3,length=20519224>\n+##contig=<ID=Chr4,length=13065296>\n+##contig=<ID=Chr5,length=18825850>\n+##contig=<ID=Chr6,length=18208465>\n+##contig=<ID=Chr7,length=18704015>\n+##contig=<ID=Chr8,length=21083321>\n+##contig=<ID=Chr9,length=11598160>\n+##contig=<ID=Unknow,length=177361715>\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">\n+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">\n+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">\n+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">\n+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">\n+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">\n+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">\n+##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">\n+##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">\n+##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">\n+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">\n+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">\n+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">\n+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">\n+##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads">\n+##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias">\n+##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples">\n+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. 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| b |
| diff -r be070a68521e -r b321e0517be3 test-data/mpileup_vcf_to_gff_output.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup_vcf_to_gff_output.gff Thu May 22 20:30:19 2014 -0400 |
| b |
| b'@@ -0,0 +1,436 @@\n+#gff-version 3\n+Chr1\tSAMTOOLS\tSNP\t14086\t14086\t31.5\t.\t.\tID=Chr1:SNP:14086;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14087\t14087\t26\t.\t.\tID=Chr1:SNP:14087;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14088\t14088\t31.5\t.\t.\tID=Chr1:SNP:14088;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14089\t14089\t31.5\t.\t.\tID=Chr1:SNP:14089;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14090\t14090\t31.5\t.\t.\tID=Chr1:SNP:14090;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14091\t14091\t26\t.\t.\tID=Chr1:SNP:14091;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14092\t14092\t26\t.\t.\tID=Chr1:SNP:14092;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14093\t14093\t31.5\t.\t.\tID=Chr1:SNP:14093;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14094\t14094\t31.5\t.\t.\tID=Chr1:SNP:14094;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14095\t14095\t31.5\t.\t.\tID=Chr1:SNP:14095;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14096\t14096\t31.5\t.\t.\tID=Chr1:SNP:14096;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14097\t14097\t31.5\t.\t.\tID=Chr1:SNP:14097;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14098\t14098\t31.5\t.\t.\tID=Chr1:SNP:14098;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14099\t14099\t31.5\t.\t.\tID=Chr1:SNP:14099;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14100\t14100\t31.5\t.\t.\tID=Chr1:SNP:14100;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14101\t14101\t31.5\t.\t.\tID=Chr1:SNP:14101;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14102\t14102\t31.5\t.\t.\tID=Chr1:SNP:14102;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14103\t14103\t26\t.\t.\tID=Chr1:SNP:14103;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14104\t14104\t31.5\t.\t.\tID=Chr1:SNP:14104;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14105\t14105\t26\t.\t.\tID=Chr1:SNP:14105;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14106\t14106\t31.5\t.\t.\tID=Chr1:SNP:14106;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14107\t14107\t31.5\t.\t.\tID=Chr1:SNP:14107;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14108\t14108\t31.5\t.\t.\tID=Chr1:SNP:14108;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14109\t14109\t31.5\t.\t.\tID=Chr1:SNP:14109;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14110\t14110\t31.5\t.\t.\tID=Chr1:SNP:14110;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14111\t14111\t31.5\t.\t.\tID=Chr1:SNP:14111;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14112\t14112\t31.5\t.\t.\tID=Chr1:SNP:14112;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14113\t14113\t31.5\t.\t.\tID=Chr1:SNP:14113;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14114\t14114\t31.5\t.\t.\tID=Chr1:SNP:14114;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14115\t14115\t31.5\t.\t.\tID=Chr1:SNP:14115;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14116\t14116\t31.5\t.\t.\tID=Chr1:SNP:14116;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14117\t14117\t31.5\t.\t.\tID=Chr1:SNP:14117;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14118\t14118\t31.5\t.\t.\tID=Chr1:SNP:14118;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t14119\t14119\t26\t.\t.\tID=Chr1:SNP:14119;Variant_seq=.;Reference_s'..b'ence_seq=C;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072448\t1072448\t31.5\t.\t.\tID=Chr1:SNP:1072448;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072449\t1072449\t26\t.\t.\tID=Chr1:SNP:1072449;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072450\t1072450\t31.5\t.\t.\tID=Chr1:SNP:1072450;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072451\t1072451\t26\t.\t.\tID=Chr1:SNP:1072451;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072452\t1072452\t31.5\t.\t.\tID=Chr1:SNP:1072452;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072453\t1072453\t26\t.\t.\tID=Chr1:SNP:1072453;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072454\t1072454\t26\t.\t.\tID=Chr1:SNP:1072454;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072455\t1072455\t26\t.\t.\tID=Chr1:SNP:1072455;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072456\t1072456\t31.5\t.\t.\tID=Chr1:SNP:1072456;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072457\t1072457\t31.5\t.\t.\tID=Chr1:SNP:1072457;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072458\t1072458\t31.5\t.\t.\tID=Chr1:SNP:1072458;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072459\t1072459\t26\t.\t.\tID=Chr1:SNP:1072459;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072460\t1072460\t31.5\t.\t.\tID=Chr1:SNP:1072460;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072461\t1072461\t31.5\t.\t.\tID=Chr1:SNP:1072461;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tINDEL\t1072461\t1072462\t33.5\t.\t.\tID=Chr1:INDEL:1072461;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072462\t1072462\t31.5\t.\t.\tID=Chr1:SNP:1072462;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072463\t1072463\t31.5\t.\t.\tID=Chr1:SNP:1072463;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072464\t1072464\t31.5\t.\t.\tID=Chr1:SNP:1072464;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072465\t1072465\t31.5\t.\t.\tID=Chr1:SNP:1072465;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072466\t1072466\t31.5\t.\t.\tID=Chr1:SNP:1072466;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072467\t1072467\t32\t.\t.\tID=Chr1:SNP:1072467;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072468\t1072468\t32.4\t.\t.\tID=Chr1:SNP:1072468;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072469\t1072469\t32.4\t.\t.\tID=Chr1:SNP:1072469;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072470\t1072470\t32.4\t.\t.\tID=Chr1:SNP:1072470;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072471\t1072471\t32.4\t.\t.\tID=Chr1:SNP:1072471;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072472\t1072472\t32.4\t.\t.\tID=Chr1:SNP:1072472;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072473\t1072473\t32.4\t.\t.\tID=Chr1:SNP:1072473;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072474\t1072474\t32.4\t.\t.\tID=Chr1:SNP:1072474;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072475\t1072475\t32.4\t.\t.\tID=Chr1:SNP:1072475;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072476\t1072476\t32.4\t.\t.\tID=Chr1:SNP:1072476;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072477\t1072477\t32.4\t.\t.\tID=Chr1:SNP:1072477;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n+Chr1\tSAMTOOLS\tSNP\t1072478\t1072478\t32.4\t.\t.\tID=Chr1:SNP:1072478;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA \n' |
| b |
| diff -r be070a68521e -r b321e0517be3 test-data/targets --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targets Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -0,0 +1,5 @@ +k69_93535:SAMTOOLS:SNP:1147 +k69_93535:SAMTOOLS:SNP:1336 +k69_98089:SAMTOOLS:SNP:30 +k69_98089:SAMTOOLS:SNP:550 +k69_98089:SAMTOOLS:SNP:625 |
| b |
| diff -r be070a68521e -r b321e0517be3 test-data/targets.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targets.fasta Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -0,0 +1,44 @@ +>k69_93535 +TCATCAAATTTATCAAATTTTCCGCAGTTTCTCGCCCTCTCCACAGCGCTTTGAAGCGCT +TTTAATGGCAGCAGATGCCGCCTCAGATCTCCCAAACCGACCCATTCCTAACACTCTCAG +AAGATCCGATTCCAATTCCGTTCTACTGAACAAATACGAGCTGGGCAAGCTCCTCGGCCA +TGGAAATTTCGCCAAGGTTTACCTCGCCCGCAACCTCGCCTCCAACGAAGAAGTCGCTAT +CAAAGTCTTCGACAAAGAGAAAATCCTCAAATCCGGCCTCGTCAACCACACCAAACGCGA +GATCTCAATCCTCCGCCGTCTTCGTCATCCGAACGTCGTCGAGCTCTTCGAGGTCATGGC +CACTAAATCGAAGATCTATTTCGTCATAGAGTACGTCCGCGGTGGTGAATTATTCGGCAA +GGTAGCCAAAGGACGTCTCAACGAAAACACCGCAAGAAAGTACTTCCAGCAATTGATTTC +CGCCGTTGATTTCTGCCACGCCAGAGGCGTTTACCACAGAGATCTGAAGCCGGAAAATTT +ATTATTAGACGATAATGGTGATTTGAAGGTGTCGGATTTCGGATTGAGCGCTGTATCGGA +CCAGATGAGGCAGGATGGGTTGTTTCACACGTTTTGTGGTACTCCAGCCTACGTTGCTCC +AGAGGTTCTCGGAAGGAAAGGGTATGATGGGGCTAAGTTTGATATTTGGTCATGTGGTGT +TATTTTGTTTTTGTTGATGGCAGGGTATTTGCCCTTTCATGATCAAAATGTGATGGCTAT +GTATAAGAAGATTTATAAAGGGGAGTTCAGGTGTCCGAGATGGTTTTCAAAGGATTTGAC +ATTGTTGCTGATGAGGCTTCTCGATACAAATCCCAAAACCCGGATCACTATTCCAGAAAT +AATGGAGAATAGATGGTTCAAGAATGGATTCGAGCCTGTGAAATATTACATTGAGAATGA +TAGGTTTCATAAGTGGTGTAGCTTAGACGAAGAGAATGCTAATGACAACGAGGAGGTAGA +ATCTGGAGATGAATCAGACTCTTCAGTTGCTTCCTGCCCTCCTACACTTAATGAAGGAAA +GAAAAAAAGGACAGGGAAGCTTCATAGGCCTTTGAGTCTGAACGCATTTGACATAATTTC +CTTTTCCAGAGGATTTGATCTTTCAGGTTTGTTTGAAGAAACGGGAGATGAAACAAGATT +TGTGTCGGGTGAAACGATACCAAACATCATATCGAAATTGGAGGAGATTGCAAAAGTGGG +TAGTTTCACGTTTAGGAAGAAGGATTGTAGGGTTAGTTTAGAAGGAACGCGAGAAGGAGT +GAAGGGCCCTCTTACGATTGGAGCTGAGATATTTGAGCTTACGCCTAGTTTGGTTGTTGT +TGAGCTTAAGAAGAAAGCAGGAGACAAAGCAGAGTACGAGGAGTTTTGTAACAAGGAGTT +GAAACCTGGGTTGCTACATCTCATGTTTCCTAATGGCGGTGTTCCTTCCAACACAACTTC +TGATACAGAGTAGGCAGTGTAGGGAATTCTCAAATGTATCTGTATTATATGGCAGCGTTT +CATGATTCTTTTTGTATTAGATTTGTCGCAAGAAATTTATGTACCTTAAGATGAAAATTC +AAGTTTCA +>k69_98089 +ACAAATCCAAACATGTTATCTTCTTCTTCTTTTCCTTCTTCAAACATCCTCCTCCTCACC +AAGTCAAAATCGCTCAACGTCAGATCATCAACACGAACTTGCGCCATGGCCACCACTGCT +TCCCCATCTCCGTACGACGTGCTAGGCCTTTCGAAAGCCGCAAACTACAGCGACATAAAA +GCAGCGTATCGGAAACTGGTGCTCTCCTGCCATCCCGATGTCTGCAAACAGCCGGATGCG +TCACCGGACGAGTTTATGAAAATACACGATGCGTATTCCACGCTTTCTGATCCGGACAAG +CGTGCCGATTACGATCGGGGAAATTCATTTGGGCGTTTGAGTTATGTGAGATCTAGATCT +GCGAATTATGGTGCTCGTCGTCGAACTTGGGAGACCGATCAGTGTTGGTAAATCTAATTT +GGGGGTTTGGAGATCTATTGATTTTGTTAGGAATGGAGAAGGTCGAGGTCAGCGGTCAGC +TACGTGGGGCTAAATATTTTGAATTGATACTGAAATTCGGGAAGACTGAAAGAACGGGAT +GATAACGGTGGTAGATCCAATTAGATTGTGGAAACTTTCATGTATGCTATCTACCTAAAA +ATAATTGTGAATTTTGTGCCTCATAAGTTTGTTTGTTTAGGCATTTTTTGACTTCTGAGA +CGTTGTATGTATATTCGGCCGTTACTACTTTATTGGCTTTAATGGTGTATACTTTGTTGT +TTGCTTGTTATCCTGTACTAAATTTCT + |
| b |
| diff -r be070a68521e -r b321e0517be3 test-data/targets.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targets.gff Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -0,0 +1,31 @@ +k69_93535 SAMTOOLS INDEL 3 7 4.44 . . ID=k69_93535:SAMTOOLS:INDEL:3;Variant_seq=ATTTCACATCCCATCATCA,ATCACATCCCATCATCA;Reference_seq=ATCA;INDEL;DP=5;VDB=0.0149;AF1=1;AC1=24;DP4=0,0,3,0;MQ=23;FQ=-33.2 +k69_93535 SAMTOOLS INDEL 5 6 4.91 . . ID=k69_93535:SAMTOOLS:INDEL:5;Variant_seq=CTCATATCCCATCATC,CCGGCC;Reference_seq=C;INDEL;DP=6;VDB=0.0137;AF1=1;AC1=24;DP4=0,0,3,1;MQ=17;FQ=-32.4 +k69_93535 SAMTOOLS SNP 1141 1142 999 . . ID=k69_93535:SAMTOOLS:SNP:1141;Variant_seq=T;Reference_seq=C;DP=2644;VDB=0.0374;AF1=0.1882;AC1=5;DP4=748,786,225,294;MQ=42;FQ=999;PV4=0.037,0,0.036,0.39 +k69_93535 SAMTOOLS SNP 1147 1148 999 . . ID=k69_93535:SAMTOOLS:SNP:1147;Variant_seq=G;Reference_seq=C;DP=2645;VDB=0.0371;AF1=0.3527;G3=0.2771,0.7229,6.934e-153;HWE=0.0248;AC1=8;DP4=733,804,447,519;MQ=42;FQ=999;PV4=0.51,0,0.027,1 +k69_93535 SAMTOOLS SNP 1336 1337 999 . . ID=k69_93535:SAMTOOLS:SNP:1336;Variant_seq=A;Reference_seq=G;DP=2211;VDB=0.0395;AF1=0.4583;G3=0.08329,0.9167,1.041e-76;HWE=0.000925;AC1=11;DP4=487,645,470,542;MQ=35;FQ=999;PV4=0.12,0,0.00016,0.36 +k69_93535 SAMTOOLS SNP 3 4 27.6 . . ID=k69_93535:SAMTOOLS:SNP:3;Variant_seq=T;Reference_seq=A;DP=5;VDB=0.0198;AF1=1;AC1=24;DP4=1,0,3,1;MQ=19;FQ=-24.6;PV4=1,1,1,1 +k69_93535 SAMTOOLS SNP 661 662 999 . . ID=k69_93535:SAMTOOLS:SNP:661;Variant_seq=G;Reference_seq=A;DP=1941;VDB=0.0388;AF1=0.4584;G3=0.08304,0.917,5.651e-77;HWE=0.000923;AC1=11;DP4=553,528,368,347;MQ=42;FQ=999;PV4=0.92,0,1,1 +k69_93535 SAMTOOLS SNP 751 752 999 . . ID=k69_93535:SAMTOOLS:SNP:751;Variant_seq=A;Reference_seq=G;DP=1870;VDB=0.0363;AF1=0.5;G3=3.472e-15,1,5e-52;HWE=4.53e-05;AC1=12;DP4=512,544,345,364;MQ=42;FQ=999;PV4=0.96,6.1e-38,0.014,1 +k69_93535 SAMTOOLS SNP 887 888 999 . . ID=k69_93535:SAMTOOLS:SNP:887;Variant_seq=G;Reference_seq=A;DP=2583;VDB=0.0394;AF1=0.4583;G3=0.08333,0.9167,8.95e-52;HWE=0.000926;AC1=11;DP4=790,493,590,361;MQ=42;FQ=999;PV4=0.83,0.069,0.41,1 +k69_98089 SAMTOOLS INDEL 2 6 999 . . ID=k69_98089:SAMTOOLS:INDEL:2;Variant_seq=CAACAAA,CAAACAAA,CAAAAACAAA;Reference_seq=CAAA;INDEL;DP=430;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,182,1;MQ=39;FQ=-71.8 +k69_98089 SAMTOOLS INDEL 3 6 999 . . ID=k69_98089:SAMTOOLS:INDEL:3;Variant_seq=AAAAAACAAA,AAAA;Reference_seq=AAA;INDEL;DP=451;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,214,1;MQ=39;FQ=-48 +k69_98089 SAMTOOLS INDEL 4 6 999 . . ID=k69_98089:SAMTOOLS:INDEL:4;Variant_seq=AAACACTAAAAACAAA,AAA;Reference_seq=AA;INDEL;DP=468;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,219,1;MQ=39;FQ=-49.3 +k69_98089 SAMTOOLS INDEL 5 6 999 . . ID=k69_98089:SAMTOOLS:INDEL:5;Variant_seq=AACTAAAAACAAA;Reference_seq=A;INDEL;DP=534;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,220,1;MQ=39;FQ=-77.6 +k69_98089 SAMTOOLS INDEL 722 723 131 . . ID=k69_98089:SAMTOOLS:INDEL:722;Variant_seq=TAAAAAA;Reference_seq=T;INDEL;DP=220;VDB=0.0006;AF1=0.3195;G3=0.299,0.701,1.118e-32;HWE=0.0406;AC1=8;DP4=4,52,0,27;MQ=38;FQ=133;PV4=0.3,1,5.4e-16,0.00096 +k69_98089 SAMTOOLS INDEL 726 727 69.7 . . ID=k69_98089:SAMTOOLS:INDEL:726;Variant_seq=TAAAAA;Reference_seq=T;INDEL;DP=152;VDB=0.0007;AF1=0.2294;AC1=5;DP4=4,30,1,6;MQ=40;FQ=70.8;PV4=1,0.025,0.0063,0.079 +k69_98089 SAMTOOLS INDEL 729 731 71.6 . . ID=k69_98089:SAMTOOLS:INDEL:729;Variant_seq=TAAAAAAA;Reference_seq=TA;INDEL;DP=104;VDB=0.0010;AF1=0.3359;AC1=8;DP4=3,15,0,4;MQ=40;FQ=73.4;PV4=1,1,1,1 +k69_98089 SAMTOOLS INDEL 741 748 48.2 . . ID=k69_98089:SAMTOOLS:INDEL:741;Variant_seq=AATTTCTATTTGTTTATTATTTCT,AATTTCTATTTGTTTATTTCT,AATTTCTATTTCT;Reference_seq=AATTTCT;INDEL;DP=18;VDB=0.0050;AF1=1;AC1=24;DP4=0,0,0,9;MQ=27;FQ=-35 +k69_98089 SAMTOOLS INDEL 742 748 5.8 . . ID=k69_98089:SAMTOOLS:INDEL:742;Variant_seq=ATTTTTCT,ATTTCTATTTTCT,ATTTCTATTTTTCT;Reference_seq=ATTTCT;INDEL;DP=17;VDB=0.0022;AF1=1;AC1=24;DP4=0,0,0,3;MQ=36;FQ=-31.8 +k69_98089 SAMTOOLS INDEL 743 748 86.5 . . ID=k69_98089:SAMTOOLS:INDEL:743;Variant_seq=TTTCTATTTGTTCT,TTTCTATTTGTTTATTATTCT,TTTCTATTTGTTTATTCT;Reference_seq=TTTCT;INDEL;DP=16;VDB=0.0021;AF1=1;AC1=24;DP4=0,0,0,8;MQ=29;FQ=-34.7 +k69_98089 SAMTOOLS SNP 2 3 999 . . ID=k69_98089:SAMTOOLS:SNP:2;Variant_seq=A;Reference_seq=C;DP=430;VDB=0.0000;AF1=0.5;G3=1.09e-24,1,5.6e-21;HWE=4.53e-05;AC1=12;DP4=207,1,212,1;MQ=40;FQ=999;PV4=1,1,0.00045,1 +k69_98089 SAMTOOLS SNP 30 31 999 . . ID=k69_98089:SAMTOOLS:SNP:30;Variant_seq=G;Reference_seq=T;DP=1858;VDB=0.0011;AF1=0.5417;G3=2.023e-19,0.9167,0.08333;HWE=0.000926;AC1=13;DP4=624,74,985,116;MQ=41;FQ=999;PV4=1,0,0.00089,1 +k69_98089 SAMTOOLS SNP 3 4 999 . . ID=k69_98089:SAMTOOLS:SNP:3;Variant_seq=C;Reference_seq=A;DP=451;VDB=0.0000;AF1=0.5;G3=3.935e-24,1,2.231e-22;HWE=4.53e-05;AC1=12;DP4=226,8,205,1;MQ=40;FQ=999;PV4=0.041,1,0.00055,1 +k69_98089 SAMTOOLS SNP 453 454 31.2 . . ID=k69_98089:SAMTOOLS:SNP:453;Variant_seq=T;Reference_seq=A;DP=3692;VDB=0.0394;AF1=0.04171;AC1=1;DP4=649,868,130,171;MQ=39;FQ=31.4;PV4=0.9,0,2.3e-293,0.00051 +k69_98089 SAMTOOLS SNP 515 516 999 . . ID=k69_98089:SAMTOOLS:SNP:515;Variant_seq=G;Reference_seq=A;DP=4455;VDB=0.0378;AF1=0.4583;G3=0.08333,0.9167,1.498e-16;HWE=0.000926;AC1=11;DP4=952,817,1390,1120;MQ=33;FQ=999;PV4=0.32,0,0,1 +k69_98089 SAMTOOLS SNP 522 523 999 . . ID=k69_98089:SAMTOOLS:SNP:522;Variant_seq=G;Reference_seq=A;DP=4698;VDB=0.0388;AF1=0.4168;G3=0.1656,0.8344,2.693e-36;HWE=0.00483;AC1=10;DP4=958,914,1327,1222;MQ=35;FQ=999;PV4=0.56,0,0,1 +k69_98089 SAMTOOLS SNP 550 551 999 . . ID=k69_98089:SAMTOOLS:SNP:550;Variant_seq=A;Reference_seq=G;DP=4866;VDB=0.0385;AF1=0.5417;G3=2.024e-12,0.9167,0.08333;HWE=0.000926;AC1=13;DP4=1034,806,1547,1233;MQ=38;FQ=999;PV4=0.72,0,1e-231,1 +k69_98089 SAMTOOLS SNP 625 626 999 . . ID=k69_98089:SAMTOOLS:SNP:625;Variant_seq=G;Reference_seq=A;DP=3557;VDB=0.0340;AF1=0.5;G3=8.721e-11,1,5.503e-15;HWE=4.53e-05;AC1=12;DP4=478,825,742,1369;MQ=41;FQ=999;PV4=0.38,0,2.7e-35,0.0059 +k69_98089 SAMTOOLS SNP 693 694 999 . . ID=k69_98089:SAMTOOLS:SNP:693;Variant_seq=A;Reference_seq=T;DP=743;VDB=0.0038;AF1=0.5;G3=1.826e-14,1,3.643e-17;HWE=4.53e-05;AC1=12;DP4=37,238,66,367;MQ=39;FQ=999;PV4=0.58,6.3e-295,5.1e-12,1 +k69_98089 SAMTOOLS SNP 717 718 999 . . ID=k69_98089:SAMTOOLS:SNP:717;Variant_seq=C;Reference_seq=T;DP=284;VDB=0.0010;AF1=0.5001;G3=2.555e-19,1,4.593e-12;HWE=4.54e-05;AC1=12;DP4=5,91,8,138;MQ=36;FQ=999;PV4=1,1.9e-90,2.7e-07,6.5e-05 +k69_98089 SAMTOOLS SNP 723 724 999 . . ID=k69_98089:SAMTOOLS:SNP:723;Variant_seq=A;Reference_seq=G;DP=193;VDB=0.0010;AF1=0.4433;G3=0.08685,0.9132,1.287e-11;HWE=0.0015;AC1=11;DP4=5,79,5,45;MQ=37;FQ=999;PV4=0.5,2.9e-13,0.00011,0.47 +k69_98089 SAMTOOLS SNP 726 727 999 . . ID=k69_98089:SAMTOOLS:SNP:726;Variant_seq=C;Reference_seq=T;DP=152;VDB=0.0008;AF1=0.4943;G3=0.0835,0.8466,0.06993;HWE=0.0149;AC1=12;DP4=4,49,5,32;MQ=36;FQ=999;PV4=0.48,5.3e-32,0.00016,0.43 |
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| diff -r be070a68521e -r b321e0517be3 umelt_service.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/umelt_service.py Thu May 22 20:30:19 2014 -0400 |
| [ |
| @@ -0,0 +1,44 @@ +#!/usr/bin/env python + +##interrogate umelt service at Univ of Utah +import sys +import urllib +import urllib2 +import xml.etree.ElementTree as ET +import numpy as np +import scipy as sp +from scipy import interpolate +from scipy.interpolate import interp1d + + +url='https://www.dna.utah.edu/db/services/cgi-bin/udesign.cgi' +timeout_sec=500 ## default for timeout + +# Query UW melt prediction service for a single sequence, returning default array for helicity, assuming within temperature range of 65-95 +def getmelt(input_seq): + values = {'seq' : input_seq, 'rs':0, 'dmso':0,'cation': 20 ,'mg': 2} # Note the buffer conditions + data = urllib.urlencode(values) + req = urllib2.Request(url, data) + try: + response = urllib2.urlopen(req,timeout=timeout_sec) + except urllib2.HTTPError, e: + print 'The server couldn\'t fulfill the request.' + print 'Error code: ', e.code + except urllib2.URLError, e: + print 'We failed to reach a server.' + print 'Reason: ', e.reason + else: + melt_data = response.read() + tree = ET.fromstring(melt_data) + helicity = [amp.find('helicity').text.split() for amp in tree.findall('amplicon')] + hels = np.array(helicity[0], dtype=np.float32).transpose() + return hels + +# helicity[0] used because the default retreived data is a list of 3 lists (for WT, mu and hets). The 3 lists are identical for our data (no IUPAC) so only [0] is used. + +def getTm(hel_array): + temps=np.arange(65,100.5,0.5) # Temperature range of 65-100.5. Step of 0.5 NEEDS TO BE CHECKED..REcent change? + tck = interpolate.splrep(temps,hel_array,s=0) + xnew =np.arange(65,95.5,0.05) + yder = interpolate.splev(xnew,tck,der=1) # der=1, first derivative + return xnew[yder.argmin()] # Returns the x value corresponding to the minimum (peak) y value -> Tm |
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| diff -r be070a68521e -r b321e0517be3 uniq.xml --- a/uniq.xml Thu Oct 18 19:47:07 2012 -0400 +++ b/uniq.xml Thu May 22 20:30:19 2014 -0400 |
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| @@ -8,5 +8,3 @@ <outputs> <data format="txt" name="outputfile" /> </outputs> - -</tool> |
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| diff -r be070a68521e -r b321e0517be3 vcf2gvf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2gvf.py Thu May 22 20:30:19 2014 -0400 |
| [ |
| @@ -0,0 +1,68 @@ +#!/usr/bin/env python +""" +Usage vcf2gvf.py <vcf_file input> <gff_file output> +""" +import sys,re + +##simplify the variant descriptor for GVF +def get_vartype(type_str): + type_str=type_str.upper() + for V in ['COMPLEX', 'MNP', 'DEL', 'INDEL','INS','SNP']: + if V in type_str: + return V + break + + + +in_vcf_file = open(sys.argv[1], 'r') +out_gff_file = open(sys.argv[2], 'w') +out_gff_file.write("#gff-version 3\n") ####gvf-version 1.06 + +##only deal with tidy source lines, samtools is special needs +source_pat = re.compile('##source=(\S+)', re.IGNORECASE) + + +while True: + line=in_vcf_file.readline() + if line[0]!='#': + break + elif line[2:10]=='samtools': + source_type='SAMTOOLS' + break + else: + m=source_pat.match(line) + if m: + source_type=m.group(1).upper() + break + + +##now read the data +##samtools only distinguishes SNPs and indels +##This is much complicated in highly heterozygous systems +##see http://www.sequenceontology.org/miso/current_release/term/SO:0001059 +##GVF column 3 requires a type from this ontology +###vcf type may be snp, mnp, ins, del, or complex. +##for current purposes map multiple types to most complex state +##ie SNP,SNP -> SNP; SNP,MNP-> MNP; SNP,complex +try: + for line in in_vcf_file: + if line[0] != '#': + var=line.split() ##see if var[7] has indel at start. If so add TYPE=INDEL for samtools case + info_field=var[7].split(';') + if info_field[0]=='INDEL': + info_field[0]="TYPE=INDEL" + info_dict=dict(X.split('=') for X in info_field) + ##if no TYPE key, then add TYPE=SNP for samtools case + if not info_dict.has_key('TYPE'): + info_dict['TYPE']='SNP'; + var_type=get_vartype(info_dict['TYPE']) + ID=":".join([var[0],source_type,var_type,var[1]]) + start=int(var[1]) + length=len(var[3]) ## using reference length in this case + attributes=";".join(['ID='+ID,'Reference_seq='+var[3],'Variant_seq='+var[4]]) + output_line=[var[0], source_type, var_type, str(start), str(start+length-1) ,'.','.','.',attributes,"\n"] + out_gff_file.write("\t".join([str(X) for X in output_line])) +finally: + in_vcf_file.close() + out_gff_file.close() + |
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| diff -r be070a68521e -r b321e0517be3 vcf2gvf.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2gvf.sh Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -0,0 +1,47 @@ +#!/bin/sh +##convert vcf to gvf +##NOTE This is a very simple basic parser for a complex format. +#It is intended for use with mpileup output where -g or -u flags are NOT used. + +##usage vcf2gvf.sh <vcf file> <outputfile> + +#Copyright 2012 John McCallum & Leshi Chen +#New Zealand Institute for Plant and Food Research + +#New Zealand Institute for Plant and Food Research +#This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + + + +inputfile=$1 +outputfile=$2 + +echo "##gvf-version 1.05" > $outputfile + +awk ' +BEGIN {OFS="\t"} + +##get feature type +{if (index($8,"INDEL")== 1) {type="INDEL"} else {type="SNP"} } +##get feature length +{if (type=="SNP") + {feat_length=1} + else {feat_length=length($4)} +} +{end=($2+feat_length)} + +!/^#/ { print $1 ,"SAMTOOLS",type,$2,end,$6,".",".","ID="$1":SAMTOOLS:"type":"$2";Variant_seq="$5";Reference_seq="$4";"$8} + +END {print ""} +' "$inputfile" > "$outputfile" \ No newline at end of file |
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| diff -r be070a68521e -r b321e0517be3 vcf2gvf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2gvf.xml Thu May 22 20:30:19 2014 -0400 |
| b |
| @@ -0,0 +1,58 @@ +<?xml version="1.0"?> +<tool id="vcf2gvf_1" name="VCF to GFF3"> + <description>convert vcf to gvf/gff3</description> + <command interpreter="bash">vcf2gvf.sh $inputFile $outputfile</command> + <inputs> + <param format="vcf" name="inputFile" type="data" label="Input vcf File" help="vcf file from mpileup" /> + </inputs> + <outputs> +<data format="gff3" name="outputfile" /> + + </outputs> +<help> +This tool provides a simple conversion from vcf to gvf. + +It is intended for use with Freebayes or with Samtools mpileup + +Be sure to read the documentation to determine if it meets your requirements. + +* vcf documentation at http://samtools.sourceforge.net/samtools.shtml#6 +* GVF/GFF3 at http://www.sequenceontology.org/resources/gvf.html +* Freebayes https://github.com/ekg/freebayes + + + +**input** + +:: + + PGSC0003DMB000000010 2042429 . C A 44.6 . DP=10;VDB=0.0118;AF1=0.8295;AC1=7;DP4=2,1,3,4;MQ=20;FQ=8.78;PV4=1,5.2e-10,1,1 GT:PL:DP:GQ 0/1:14,0,42:5:23 1/1:27,6,0:2:9 1/1:15,3,0:1:7 1/1:30,6,0:2:9 + PGSC0003DMB000000038 1756646 . G A 3.69 . DP=15;VDB=0.0166;AF1=0.495;AC1=4;DP4=3,7,2,2;MQ=20;FQ=5.6;PV4=0.58,3.8e-09,1,0.31 GT:PL:DP:GQ 0/1:20,3,0:1:6 0/1:9,0,67:7:8 0/0:0,15,82:5:17 0/1:16,3,0:1:5 + PGSC0003DMB000000064 1916664 . T C 8.12 . DP=4;VDB=0.0151;AF1=1;AC1=8;DP4=0,0,0,3;MQ=20;FQ=-29.5 GT:PL:DP:GQ 1/1:14,3,0:1:5 1/1:0,0,0:0:3 1/1:13,3,0:1:5 1/1:15,3,0:1:5 + + +**output** + + +:: + + PGSC0003DMB000000010 samtools SNP 2042429 2042430 44.6 . . ID=PGSC0003DMB000000010:SAMTOOLS:SNP:2042429;Variant_seq=A;Reference_seq=C;DP=10;VDB=0.0118;AF1=0.8295;AC1=7;DP4=2,1,3,4;MQ=20;FQ=8.78;PV4=1,5.2e-10,1,1 + PGSC0003DMB000000038 samtools SNP 1756646 1756647 3.69 . . ID=PGSC0003DMB000000038:SAMTOOLS:SNP:1756646;Variant_seq=A;Reference_seq=G;DP=15;VDB=0.0166;AF1=0.495;AC1=4;DP4=3,7,2,2;MQ=20;FQ=5.6;PV4=0.58,3.8e-09,1,0.31 + PGSC0003DMB000000064 samtools SNP 1916664 1916665 8.12 . . ID=PGSC0003DMB000000064:SAMTOOLS:SNP:1916664;Variant_seq=C;Reference_seq=T;DP=4;VDB=0.0151;AF1=1;AC1=8;DP4=0,0,0,3;MQ=20;FQ=-29.5 + + + +----------------------- + +*If you use this tool please cite:* + +A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: +Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.) +(2012) + +Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, +Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum + + +</help> +</tool> |
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| diff -r be070a68521e -r b321e0517be3 vcf_gff.py --- a/vcf_gff.py Thu Oct 18 19:47:07 2012 -0400 +++ b/vcf_gff.py Thu May 22 20:30:19 2014 -0400 |
| [ |
| @@ -46,6 +46,8 @@ record_type = "SNP" for entry in rec: detail = entry.split("=") + if len(detail) < 2: + continue INFO[detail[0]] = detail[1] if INFO.has_key("DP"): reads = INFO.get("DP") @@ -108,7 +110,9 @@ gen = "HET" if genotypes == "0/0": gen = "HOM_ref" - else: + try: # set gen to 'NA' if still unset + gen + except NameError: gen = "NA" geno = ("%s:%s " % (reads, gen)) genos += geno @@ -141,11 +145,11 @@ end = start gen = get_gen(info[8:], reference) out_gff_file.write( - ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%d;Variant" + + ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%s:%d;Variant" + "_seq=%s;Reference_seq=%s;Total_reads=%s;Zygosity=%s\n") % ( seqid, source,record_type, start, end, score, strand, phase,seqid, - record_type, start, variant, reference, reads, gen)) - + source, record_type, start, variant, reference, reads, gen)) + out_gff_file.close() |
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| diff -r be070a68521e -r b321e0517be3 vcf_gff.xml --- a/vcf_gff.xml Thu Oct 18 19:47:07 2012 -0400 +++ b/vcf_gff.xml Thu May 22 20:30:19 2014 -0400 |
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| @@ -8,6 +8,16 @@ <outputs> <data format="gff3" name="outputfile" /> </outputs> + <tests> + <test> + <param name="inputVcf" value="mpileup_out.vcf" ftype="vcf"/> + <output name="outputfile" file="mpileup_vcf_to_gff_output.gff"/> + </test> + <test> + <param name="inputVcf" value="freebayes_out.vcf" ftype="vcf"/> + <output name="outputfile" file="freebayes_vcf_to_gff_output.gff"/> + </test> + </tests> <help> ** Convert vcf to gff3** @@ -58,4 +68,4 @@ Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum </help> -</tool> \ No newline at end of file +</tool> |