AUTHOR: Matt Durrant

ASEtools

A python command line interface for preparing and analyzing allele-specific expression data ##

The main entry point is through typing

python asetools/

or

python asetools/__main__.py

You can get detailed argument instructions with python asetools/ --help

My code directories are structured as follows:

    asetools/
    ├── __main__.py
    └── mod
        |── subprocess_step_superclass.py
        ├── pipeline_superclass.py
        ├── process_step_superclass.py
        ├── config
        │   ├── custom.py
        │   └── fixed.py
        ├── misc
        │   ├── argparse_types.py
        │   ├── exceptions.py
        │   ├── integer_constants.py
        │   ├── log.py
        │   ├── path_methods.py
        │   ├── qsub.py
        │   ├── qvalue.py
        │   ├── record_classes.py
        │   ├── string_constants.py
        │   └── version_parsers.py
        ├── pipelines
        │   ├── rnaseq_variant_calling.py
        │   └── wasp_ase_pipeline.py
        ├── process
        │   ├── change_vcf_chrom.py
        │   ├── fishers_exact_test.py
        │   ├── prepare_count_data.py
        │   ├── retrieve_mapping_distances.py
        │   ├── vcf_filter_ase.py
        │   ├── vcf_summary_statistics.py
        │   └── wasp_make_snp_dir.py
        └── subprocess
            ├── add_read_groups.py
            ├── ase_read_counter.py
            ├── haplotype_caller.py
            ├── java.py
            ├── mark_duplicates.py
            ├── print_reads.py
            ├── rnaseq_base_recalibrator.py
            ├── samtools_index.py
            ├── samtools_merge.py
            ├── samtools.py
            ├── samtools_sort.py
            ├── split_n_cigar_reads.py
            ├── star_align.py
            ├── variant_filtration.py
            ├── wasp_filter_remapped_reads.py
            └── wasp_find_intersecting_snps.py

You can run the asetools CLI with command such as the following:

    python asetools Pipeline-RNAseqVariantCaller --fastq1 example_input/Pipeline-RNAseqVariantCaller.1.fq.gz --fastq2 example_input/Pipeline-RNAseqVariantCaller.2.fq.gz example_output/Pipeline-RNAseqVariantCaller

    python asetools Pipeline-ASEReadCounterWASP --bam example_input/Pipeline-ASEReadCounterWASP.bam --vcf example_input/Pipeline-ASEReadCounterWASP.vcf.gz example_output/Pipeline-ASEReadCounterWASP

    python asetools VcfFilterASE example_output/VcfFilterASE --vcf example_input/VcfFilterASE.vcf.gz

    python asetools FishersExactTest example_output/FishersExactTest --read-counts example_input/FishersExactTest.tsv

    python asetools PrepareReadCountData example_output/PrepareReadCountData --cases example_input/PrepareReadCountData.1.tsv --controls example_input/PrepareReadCountData.2.tsv

    python asetools ChangeVcfChrom --vcf example_input/ChangeVCFChrom_add_chr.vcf --add-chr example_output/ChangeVCFChrom_add_chr

    python asetools ChangeVcfChrom --vcf example_input/ChangeVCFChrom_remove_chr.vcf --remove-chr example_output/ChangeVCFChrom_remove_chr

    python asetools VcfSummaryStatistics --vcf example_input/VcfSummaryStatistics.vcf.gz example_output/VcfSummaryStatistics

    python asetools/ RetrieveMappingDistances --bam example_input/RetrieveMappingDistances.bam --vcf example_input/RetrieveMappingDistances.vcf.gz example_output/RetrieveMappingDistances