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CoVaMa_0.7.zip (3.6 MB)
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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| CoVaMa_0.7 | 2018-07-27 | ||
| ViReMa_0.7_4CoVaMa.zip | 2015-08-05 | 586.8 kB | |
| README.txt | 2015-08-05 | 11.5 kB | |
| CoVaMa_0.1.zip | 2015-08-05 | 4.3 MB | |
| Totals: 4 Items | 4.9 MB | 0 |
CoVaMa Version 0.1
Last Modified: 4-8-15
Contents:
TestData_FHV-25k (15 files)
Small test data set using 25000 reads from an FHV RNAseq experiment
- FHV_Genome_padded.?.ewbt (6 files, bowtie index)
- FHV_R1_25k.txt (Raw Reads_5'read)
- FHV_R2_25k.txt (Raw Reads_3'read)
- FHV_R1_25k_FHV-mapping.sam (FHV Genome mapping, 5' reads)
- FHV_R2_25k_FHV-mapping.sam (FHV Genome mapping, 3' reads)
- R1_ViReMa_Output.txt (No Header)
- R2_ViReMa_Output.txt (No Header)
- R1_mFHV_mDm.txt (5' reads unaligned to FHV and D.melanogaster genome)
- R1_mFHV_mDm.txt (3' reads unaligned to FHV and D.melanogaster genome)
- FHV_Genome_padded.txt Contains reference genes for Flock House Virus with long 3' terminal A residues.
CoVaMa_Make_Matrices.py
Script used to generate Nucleotide Matrices. Runs from Command-line.
CoVaMa_Make_Matrices_wAA.py
Script used to generate Amino Acid Matrices. Runs from Command-line.
CoVaMa_Merge_Matrices.py
Script used to Merge multiple matrices. Runs from Command-line.
CoVaMa_Analyse_Matrices.py
Script used to Analyse Nucleotide Matrices. Runs from Command-line.
CoVaMa_Analyse_Matrices_wAA.py
Script used to Analyse Amino Acid Matrices. Runs from Command-line.
Config.py
This script carries the global variables.
README.txt
Includes instructions to run CoVaMa.
LICENSE.txt
Copyright info.
CoVaMa is a simple python script and so should not require any special installation.
CoVaMa requires python version 2.7 and Numpy.
To analyse recombination/fusion events, CoVaMa requires the output files from ViReMa_0.7
CoVaMa is run from the command line:
>python CoVaMa_Make_Matrices.py Virus_Index Input_Data Output_Directory [args]
>python CoVaMa_Analyse_Matrices.py PickleFile Output_Data Output_Directory [args]
If amino acid sequences wish to be analyse rather than nucleotide sequences, use the '_wAA' versions of the scripts.
Open reading frames must be given in the command-line for CoVaMa_Make_Matrices_wAA.py
Currently, only one open reading frame can be used, and only one gene can be analysed.
Split the alignment data accrodingly if multiple genes are to be analysed.
Example using test data:
>python CoVaMa_Make_Matrices.py TestData TestData/FHV_Genome_padded.txt --SAM1 TestData/FHV_R1_25k_FHV-mapping.sam --ViReMa_Output TestData/R1_ViReMa_Output.txt --Min_Fusion_Coverage 10 --SAM2 TestData/FHV_R2_25k_FHV-mapping.sam --ViReMa_Output2 TestData/R2_ViReMa_Output.txt
>python CoVaMa_Analyse_Matrices.py TestData/Total_Matrices.py.pi Output.txt TestData/ --Min_Coverage 10 --Min_Fusion_Coverage 10 -OutArray -Weighted
------------------------------------------------------------------------------
CoVaMa_Make_Matrices.py
[-h] [--SAM1 SAM1] [--SAM2 SAM2]
[--ViReMa_Output VIREMA_OUTPUT]
[--ViReMa_Output2 VIREMA_OUTPUT2]
[--Min_Coverage_Output MIN_COVERAGE_OUTPUT]
[--Fusion_Exclusion FUSION_EXCLUSION]
[--Min_Fusion_Coverage MIN_FUSION_COVERAGE]
[--Ends ENDS]
Output_Dir FASTAFile
Required arguments:
Output_Dir Enter name of desired output directory
FASTAFile Enter name of Fasta reference genome used in original
sequence alignment e.g. FHV_Genome.txt
Optional arguments:
--SAM1 SAM1 Enter name of SamFile
--SAM2 SAM2 Enter name of second/paired SamFile
--ViReMa_Output VIREMA_OUTPUT
Enter name of second/paired SamFile
--ViReMa_Output2 VIREMA_OUTPUT2
Enter name of second/paired SamFile
--Fusion_Exclusion FUSION_EXCLUSION
Required number of nucleotides to exclude
recombination event. Default == 10
--Min_Fusion_Coverage MIN_FUSION_COVERAGE
Enter minimum coverage over pairs of associated
nucleotides. Default value is 1000
--Ends ENDS Enter number of nucleotides to ignore from 5' and 3'
extremities. Default value is 0
------------------------------------------------------------------------------
CoVaMa_Make_Matrices_wAA.py
[-h] [--SAM1 SAM1] [--SAM2 SAM2]
[--ViReMa_Output VIREMA_OUTPUT]
[--ViReMa_Output2 VIREMA_OUTPUT2]
[--Min_Coverage_Output MIN_COVERAGE_OUTPUT]
[--Fusion_Exclusion FUSION_EXCLUSION]
[--Min_Fusion_Coverage MIN_FUSION_COVERAGE]
[--Ends ENDS]
Output_Dir FASTAFile
Required arguments:
Output_Dir Enter name of desired output directory
FASTAFile Enter name of Fasta reference genome used in original
sequence alignment e.g. FHV_Genome.txt
ORFStartNuc Enter minimum coverage over pairs of associated
nucleotides. Default value is 1
ORFFinishNuc Enter minimum coverage over pairs of associated
nucleotides. Default value is 10000
Optional arguments:
--SAM1 SAM1 Enter name of SamFile
--SAM2 SAM2 Enter name of second/paired SamFile
--ViReMa_Output VIREMA_OUTPUT
Enter name of second/paired SamFile
--ViReMa_Output2 VIREMA_OUTPUT2
Enter name of second/paired SamFile
--Fusion_Exclusion FUSION_EXCLUSION
Required number of nucleotides to exclude
recombination event. Default == 10
--Min_Fusion_Coverage MIN_FUSION_COVERAGE
Enter minimum coverage over pairs of associated
nucleotides. Default value is 1000
--Ends ENDS Enter number of nucleotides to ignore from 5' and 3'
extremities. Default value is 0
--------------------------------------------------------------------------
CoVaMa_Merge_Matrices.py
[-h] [--Multiplier MULTIPLIER]
[--Min_Coverage MIN_COVERAGE]
PickleFiles Output_File Output_Dir
Required arguments:
PickleFiles Enter name of PickleFiles as string (e.g.: 'Total_Matrices1.py.pi Total_Matrices2.py.pi')
Output_File Enter name of desired output file
Output_Dir Enter name of desired output directory
Optional arguments:
--Multiplier MULTIPLIER
Enter integer number of reads desired per table,
Default = 1'000'000
--Min_Coverage MIN_COVERAGE
Number of mapped nucleotides per contigency table
required for merge. Default == 100
---------------------------------------------------------------------------
CoVaMa_Analyse_Matrices.py
[-h] [--Min_Coverage MIN_COVERAGE]
[--Min_Fusion_Coverage MIN_FUSION_COVERAGE]
[--Min_Pop_Fraction MIN_POP_FRACTION]
[-OutArray] [-OutAllLDs] [-Merge]
[-Weighted]
[--Min_Merged_Matrices MIN_MERGED_MATRICES]
[--LD_Precision LD_PRECISION]
PickleFile Output_File Output_Dir
Required arguments:
PickleFile Enter name of PickleFile
Output_File Enter name of desired output file
Output_Dir Enter name of desired output directory
Optional arguments:
--Min_Coverage MIN_COVERAGE
Enter minimum coverage over pairs of associated
nucleotides. Default value is 1000
--Min_Fusion_Coverage MIN_FUSION_COVERAGE
Enter minimum coverage over recombination event.
Default value is 1000
--Min_Pop_Fraction MIN_POP_FRACTION
Enter a float between 0 and 1 for the required
association fraction. Default value is 0.001.
-OutArray Write array values into output file if LD is found.
Default value is false.
-OutAllLDs Write out all LD values found. Default value is output
highest value only.
-Merge If input Matrix is from merged matrices, select
-Merge. Default is False
-Weighted Weight each LD value according to fraction of reads
from total contingency table. Default is False.
--Min_Merged_Matrices MIN_MERGED_MATRICES
Enter a minimum number of matrices required that were
used to generated merged matrix. Default value is 1.
--LD_Precision LD_PRECISION
Enter number of floating point digits for LD
output. Default value is 6.
-------------------------------------------------------------------------------
CoVaMa_Analyse_Matrices_wAA.py
[-h] [--Min_Coverage MIN_COVERAGE]
[--Min_Fusion_Coverage MIN_FUSION_COVERAGE]
[--Min_Pop_Fraction MIN_POP_FRACTION]
[-OutArray] [-OutAllLDs] [-Merge]
[-Weighted]
[--Min_Merged_Matrices MIN_MERGED_MATRICES]
[--LD_Precision LD_PRECISION]
PickleFile Output_File Output_Dir
Required arguments:
PickleFile Enter name of PickleFile
Output_File Enter name of desired output file
Output_Dir Enter name of desired output directory
Optional arguments:
--Min_Coverage MIN_COVERAGE
Enter minimum coverage over pairs of associated
nucleotides. Default value is 1000
--Min_Fusion_Coverage MIN_FUSION_COVERAGE
Enter minimum coverage over recombination event.
Default value is 1000
--Min_Pop_Fraction MIN_POP_FRACTION
Enter a float between 0 and 1 for the required
association fraction. Default value is 0.001.
-OutArray Write array values into output file if LD is found.
Default value is false.
-OutAllLDs Write out all LD values found. Default value is output
highest value only.
-Merge If input Matrix is from merged matrices, select
-Merge. Default is False
-Weighted Weight each LD value according to fraction of reads
from total contingency table. Default is False.
--Min_Merged_Matrices MIN_MERGED_MATRICES
Enter a minimum number of matrices required that were
used to generated merged matrix. Default value is 1.
--LD_Precision LD_PRECISION
Enter number of floating point digits for LD
output. Default value is 6.
-------------------------------------------------------------------------------
