From 053aea1b845c584656c91c50a1014b900ca391cd Mon Sep 17 00:00:00 2001 From: Ali Pirani Date: Wed, 19 Dec 2018 15:50:47 -0500 Subject: [PATCH] Matrix changes and GATK Indel integration --- .gitignore | 18 + .idea/workspace.xml | 194 ++-- README.md | 207 ++-- barplot.png | Bin 442748 -> 0 bytes barplot_DP.png | Bin 452495 -> 0 bytes config_ali | 49 +- config_gatk | 237 +++++ modules/beast/SCOTTI_generate_xml.py | 412 ++++++++ .../fasta_functions.cpython-35.pyc | Bin 0 -> 8056 bytes .../scotti_functions.cpython-35.pyc | Bin 0 -> 31536 bytes modules/beast/add_invariant_sites_beast.sh | 14 + modules/beast/beast.py | 102 ++ modules/beast/beast_pbs_flux.pl | 100 ++ modules/beast/change_prefixes_beast_xml.sh | 24 + modules/beast/countInvarSites.py | 56 ++ modules/beast/fasta_functions.py | 275 +++++ modules/beast/fasta_functions.pyc | Bin 0 -> 1435 bytes .../beast/generate_input_file_beast_pbs.sh | 12 + modules/beast/get_num_invariant_sites_v2.py | 89 ++ modules/beast/insert_starting_tree_beast.sh | 17 + modules/beast/scotti.py | 108 ++ modules/beast/scotti_functions.py | 759 ++++++++++++++ modules/beast/scotti_functions.py.bak | 408 ++++++++ modules/beast/scotti_functions.pyc | Bin 0 -> 30618 bytes modules/beast/test.csv | 2 + modules/beast/testfn.py | 17 + modules/cluster_based_prep/log_modules.py | 30 - .../cluster_based_prep/logging_subprocess.py | 41 - .../prep_cluster_calling.py | 97 -- modules/core_prep_sanity_checks.py | 34 +- modules/core_prep_sanity_checks.pyc | Bin 3934 -> 4050 bytes modules/gatk.py | 318 +++--- modules/gatk.pyc | Bin 12873 -> 13835 bytes modules/phage_detection.py | 22 +- modules/phage_detection.pyc | Bin 5203 -> 5607 bytes modules/remove_5_bp_snp_indel.py | 288 ++++-- modules/remove_5_bp_snp_indel.pyc | Bin 3715 -> 6467 bytes modules/stages.py | 36 +- modules/stages.pyc | Bin 10124 -> 9287 bytes modules/variant_diagnostics/DP_analysis.py | 102 +- .../R_scripts/non_core_variant_qc.R | 122 +++ .../R_scripts/render_non_core_variant_qc.R | 12 + modules/variant_diagnostics/core_pipeline.py | 939 +++++++++++++----- ...only_ref_variant_fasta_unique_positions.py | 22 +- .../mask_gubbins_variants.py | 10 +- .../reason_job_indel_debug.py | 4 +- .../reason_job_indel_debug_gatk.py | 173 ++++ .../scripts/gubbins_iqtree_raxml.sh | 52 +- .../gubbins_iqtree_raxml_backup_2018_10_31.sh | 82 ++ other/FQ_analysis.py | 78 -- other/README.md | 2 - other/__init__.py | 1 - other/allele_frequency_analysis.py | 93 -- other/config_backup | 160 --- other/config_default_21dec | 172 ---- other/config_gatk | 93 -- other/pipeline.py.save | 139 --- other/pipeline_gatk.py | 101 -- pipeline.png | Bin 229170 -> 0 bytes pipeline.py | 67 +- plots/Sample_barplot.png | Bin 227887 -> 0 bytes variant_call.py | 528 ++++++++-- variant_call_backup.py | 643 ------------ variant_call_debug.py | 651 ------------ variant_calling_pipeline_dev/other | 1 - 65 files changed, 5021 insertions(+), 3192 deletions(-) create mode 100644 .gitignore delete mode 100644 barplot.png delete mode 100644 barplot_DP.png create mode 100755 config_gatk create mode 100644 modules/beast/SCOTTI_generate_xml.py create mode 100644 modules/beast/__pycache__/fasta_functions.cpython-35.pyc create mode 100644 modules/beast/__pycache__/scotti_functions.cpython-35.pyc create mode 100755 modules/beast/add_invariant_sites_beast.sh create mode 100644 modules/beast/beast.py create mode 100755 modules/beast/beast_pbs_flux.pl create mode 100755 modules/beast/change_prefixes_beast_xml.sh create mode 100644 modules/beast/countInvarSites.py create mode 100755 modules/beast/fasta_functions.py create mode 100644 modules/beast/fasta_functions.pyc create mode 100755 modules/beast/generate_input_file_beast_pbs.sh create mode 100755 modules/beast/get_num_invariant_sites_v2.py create mode 100755 modules/beast/insert_starting_tree_beast.sh create mode 100644 modules/beast/scotti.py create mode 100644 modules/beast/scotti_functions.py create mode 100644 modules/beast/scotti_functions.py.bak create mode 100644 modules/beast/scotti_functions.pyc create mode 100644 modules/beast/test.csv create mode 100644 modules/beast/testfn.py delete mode 100644 modules/cluster_based_prep/log_modules.py delete mode 100644 modules/cluster_based_prep/logging_subprocess.py delete mode 100644 modules/cluster_based_prep/prep_cluster_calling.py create mode 100755 modules/variant_diagnostics/R_scripts/non_core_variant_qc.R create mode 100755 modules/variant_diagnostics/R_scripts/render_non_core_variant_qc.R create mode 100755 modules/variant_diagnostics/reason_job_indel_debug_gatk.py create mode 100755 modules/variant_diagnostics/scripts/gubbins_iqtree_raxml_backup_2018_10_31.sh delete mode 100755 other/FQ_analysis.py delete mode 100755 other/README.md delete mode 100755 other/__init__.py delete mode 100755 other/allele_frequency_analysis.py delete mode 100755 other/config_backup delete mode 100755 other/config_default_21dec delete mode 100755 other/config_gatk delete mode 100755 other/pipeline.py.save delete mode 100755 other/pipeline_gatk.py delete mode 100644 pipeline.png delete mode 100644 plots/Sample_barplot.png delete mode 100644 variant_call_backup.py delete mode 100644 variant_call_debug.py delete mode 160000 variant_calling_pipeline_dev/other diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..98fc96d --- /dev/null +++ b/.gitignore @@ -0,0 +1,18 @@ +modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_gubbins_masked.fa +modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_gubbins_masked_invar_site_counts.txt +modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_gubbins_masked_snp-sites.vcf +modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_gubbins_masked_var_sites.fa +modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_invar_site_counts.txt +modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_masked_recomb_positions.txt +modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_snp-sites.vcf +modules/beast/test/input_beast.txt +modules/beast/test/invar_base_counts.txt +modules/beast/test/model_finder_IQTREE_noDec_wDates_LA.tree +modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta2_renamed.xml +modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta2.xml +modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta_renamed_st_invSites.xml +modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta_renamed.xml +modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta.xml +modules/beast/test/test_commands.sh +modules/beast/test/test_fasta_path.txt +modules/beast/test/test_gff_path.txt diff --git a/.idea/workspace.xml b/.idea/workspace.xml index b54d3a9..e2df7eb 100644 --- a/.idea/workspace.xml +++ b/.idea/workspace.xml @@ -2,103 +2,7 @@ - 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