Merge pull request #3 from enriiquee/master

Renaming folder
PRIDE-Cluster · Mar 13, 2017 · b2a98d3 · b2a98d3
2 parents 7bf68bb + bbca600
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diff --git a/..._QC_Clustering.files/duplicate_remover.pl → QC_Cluster_Results/duplicate_remover.pl b/..._QC_Clustering.files/duplicate_remover.pl → QC_Cluster_Results/duplicate_remover.pl
diff --git a/..._QC_Clustering.files/duplicate_remover.py → QC_Cluster_Results/duplicate_remover.py b/..._QC_Clustering.files/duplicate_remover.py → QC_Cluster_Results/duplicate_remover.py
diff --git a/...pectra-cluster-py-comparer-dev/.gitignore → ...pectra-cluster-py-comparer-dev/.gitignore b/...pectra-cluster-py-comparer-dev/.gitignore → ...pectra-cluster-py-comparer-dev/.gitignore
diff --git a/...s/spectra-cluster-py-comparer-dev/LICENSE → ...s/spectra-cluster-py-comparer-dev/LICENSE b/...s/spectra-cluster-py-comparer-dev/LICENSE → ...s/spectra-cluster-py-comparer-dev/LICENSE
diff --git a/.../spectra-cluster-py-comparer-dev/Makefile → .../spectra-cluster-py-comparer-dev/Makefile b/.../spectra-cluster-py-comparer-dev/Makefile → .../spectra-cluster-py-comparer-dev/Makefile
diff --git a/...pectra-cluster-py-comparer-dev/README.rst → ...pectra-cluster-py-comparer-dev/README.rst b/...pectra-cluster-py-comparer-dev/README.rst → ...pectra-cluster-py-comparer-dev/README.rst
diff --git a/...tra-cluster-py-comparer-dev/docs/Makefile → ...tra-cluster-py-comparer-dev/docs/Makefile b/...tra-cluster-py-comparer-dev/docs/Makefile → ...tra-cluster-py-comparer-dev/docs/Makefile
diff --git a/...tra-cluster-py-comparer-dev/docs/make.bat → ...tra-cluster-py-comparer-dev/docs/make.bat b/...tra-cluster-py-comparer-dev/docs/make.bat → ...tra-cluster-py-comparer-dev/docs/make.bat
diff --git a/...dev/docs/source/api/abstract_analyser.rst → ...dev/docs/source/api/abstract_analyser.rst b/...dev/docs/source/api/abstract_analyser.rst → ...dev/docs/source/api/abstract_analyser.rst
diff --git a/...-dev/docs/source/api/cluster_features.rst → ...-dev/docs/source/api/cluster_features.rst b/...-dev/docs/source/api/cluster_features.rst → ...-dev/docs/source/api/cluster_features.rst
diff --git a/...dev/docs/source/api/clustering_parser.rst → ...dev/docs/source/api/clustering_parser.rst b/...dev/docs/source/api/clustering_parser.rst → ...dev/docs/source/api/clustering_parser.rst
diff --git a/...rer-dev/docs/source/api/id_transferer.rst → ...rer-dev/docs/source/api/id_transferer.rst b/...rer-dev/docs/source/api/id_transferer.rst → ...rer-dev/docs/source/api/id_transferer.rst
diff --git a/...py-comparer-dev/docs/source/api/index.rst → ...py-comparer-dev/docs/source/api/index.rst b/...py-comparer-dev/docs/source/api/index.rst → ...py-comparer-dev/docs/source/api/index.rst
diff --git a/...-comparer-dev/docs/source/api/objects.rst → ...-comparer-dev/docs/source/api/objects.rst b/...-comparer-dev/docs/source/api/objects.rst → ...-comparer-dev/docs/source/api/objects.rst
diff --git a/...uster-py-comparer-dev/docs/source/conf.py → ...uster-py-comparer-dev/docs/source/conf.py b/...uster-py-comparer-dev/docs/source/conf.py → ...uster-py-comparer-dev/docs/source/conf.py
diff --git a/...-py-comparer-dev/docs/source/contents.rst → ...-py-comparer-dev/docs/source/contents.rst b/...-py-comparer-dev/docs/source/contents.rst → ...-py-comparer-dev/docs/source/contents.rst
diff --git a/...ter-py-comparer-dev/docs/source/index.rst → ...ter-py-comparer-dev/docs/source/index.rst b/...ter-py-comparer-dev/docs/source/index.rst → ...ter-py-comparer-dev/docs/source/index.rst
diff --git a/...ocs/source/tools/cluster_features_cli.rst → ...ocs/source/tools/cluster_features_cli.rst b/...ocs/source/tools/cluster_features_cli.rst → ...ocs/source/tools/cluster_features_cli.rst
diff --git a/...v/docs/source/tools/id_transferer_cli.rst → ...v/docs/source/tools/id_transferer_cli.rst b/...v/docs/source/tools/id_transferer_cli.rst → ...v/docs/source/tools/id_transferer_cli.rst
diff --git a/...-comparer-dev/docs/source/tools/index.rst → ...-comparer-dev/docs/source/tools/index.rst b/...-comparer-dev/docs/source/tools/index.rst → ...-comparer-dev/docs/source/tools/index.rst
diff --git a/...rce/tools/mgf_search_result_annotator.rst → ...rce/tools/mgf_search_result_annotator.rst b/...rce/tools/mgf_search_result_annotator.rst → ...rce/tools/mgf_search_result_annotator.rst
diff --git a/...v/docs/source/tools/protein_annotator.rst → ...v/docs/source/tools/protein_annotator.rst b/...v/docs/source/tools/protein_annotator.rst → ...v/docs/source/tools/protein_annotator.rst
diff --git a/...-cluster-py-comparer-dev/requirements.txt → ...-cluster-py-comparer-dev/requirements.txt b/...-cluster-py-comparer-dev/requirements.txt → ...-cluster-py-comparer-dev/requirements.txt
diff --git a/...-comparer-dev/spectra_cluster/__init__.py → ...-comparer-dev/spectra_cluster/__init__.py b/...-comparer-dev/spectra_cluster/__init__.py → ...-comparer-dev/spectra_cluster/__init__.py
diff --git a/...-dev/spectra_cluster/analyser/__init__.py → ...-dev/spectra_cluster/analyser/__init__.py b/...-dev/spectra_cluster/analyser/__init__.py → ...-dev/spectra_cluster/analyser/__init__.py
diff --git a/...ctra_cluster/analyser/cluster_comparer.py → ...ctra_cluster/analyser/cluster_comparer.py b/...ctra_cluster/analyser/cluster_comparer.py → ...ctra_cluster/analyser/cluster_comparer.py
diff --git a/...ctra_cluster/analyser/cluster_features.py → ...ctra_cluster/analyser/cluster_features.py b/...ctra_cluster/analyser/cluster_features.py → ...ctra_cluster/analyser/cluster_features.py
diff --git a/...uster/analyser/cluster_filter_analyser.py → ...uster/analyser/cluster_filter_analyser.py b/...uster/analyser/cluster_filter_analyser.py → ...uster/analyser/cluster_filter_analyser.py
diff --git a/...er-dev/spectra_cluster/analyser/common.py → ...er-dev/spectra_cluster/analyser/common.py b/...er-dev/spectra_cluster/analyser/common.py → ...er-dev/spectra_cluster/analyser/common.py
diff --git a/...spectra_cluster/analyser/id_transferer.py → ...spectra_cluster/analyser/id_transferer.py b/...spectra_cluster/analyser/id_transferer.py → ...spectra_cluster/analyser/id_transferer.py
diff --git a/...-dev/spectra_cluster/clustering_parser.py → ...-dev/spectra_cluster/clustering_parser.py b/...-dev/spectra_cluster/clustering_parser.py → ...-dev/spectra_cluster/clustering_parser.py
diff --git a/...y-comparer-dev/spectra_cluster/objects.py → ...y-comparer-dev/spectra_cluster/objects.py b/...y-comparer-dev/spectra_cluster/objects.py → ...y-comparer-dev/spectra_cluster/objects.py
diff --git a/...rer-dev/spectra_cluster/tools/__init__.py → ...rer-dev/spectra_cluster/tools/__init__.py b/...rer-dev/spectra_cluster/tools/__init__.py → ...rer-dev/spectra_cluster/tools/__init__.py
diff --git a/...ev/spectra_cluster/tools/fasta_paraser.py → ...ev/spectra_cluster/tools/fasta_paraser.py b/...ev/spectra_cluster/tools/fasta_paraser.py → ...ev/spectra_cluster/tools/fasta_paraser.py
diff --git a/...mparer-dev/spectra_cluster/ui/__init__.py → ...mparer-dev/spectra_cluster/ui/__init__.py b/...mparer-dev/spectra_cluster/ui/__init__.py → ...mparer-dev/spectra_cluster/ui/__init__.py
diff --git a/...pectra_cluster/ui/cluster_comparer_cli.py → ...pectra_cluster/ui/cluster_comparer_cli.py b/...pectra_cluster/ui/cluster_comparer_cli.py → ...pectra_cluster/ui/cluster_comparer_cli.py
diff --git a/...pectra_cluster/ui/cluster_features_cli.py → ...pectra_cluster/ui/cluster_features_cli.py b/...pectra_cluster/ui/cluster_features_cli.py → ...pectra_cluster/ui/cluster_features_cli.py
diff --git a/...-dev/spectra_cluster/ui/cluster_filter.py → ...-dev/spectra_cluster/ui/cluster_filter.py b/...-dev/spectra_cluster/ui/cluster_filter.py → ...-dev/spectra_cluster/ui/cluster_filter.py
diff --git a/...v/spectra_cluster/ui/id_transferer_cli.py → ...v/spectra_cluster/ui/id_transferer_cli.py b/...v/spectra_cluster/ui/id_transferer_cli.py → ...v/spectra_cluster/ui/id_transferer_cli.py
diff --git a/...cluster/ui/mgf_search_result_annotator.py → ...cluster/ui/mgf_search_result_annotator.py b/...cluster/ui/mgf_search_result_annotator.py → ...cluster/ui/mgf_search_result_annotator.py
diff --git a/...v/spectra_cluster/ui/protein_annotator.py → ...v/spectra_cluster/ui/protein_annotator.py b/...v/spectra_cluster/ui/protein_annotator.py → ...v/spectra_cluster/ui/protein_annotator.py
diff --git a/...cluster-py-comparer-dev/tests/__init__.py → ...cluster-py-comparer-dev/tests/__init__.py b/...cluster-py-comparer-dev/tests/__init__.py → ...cluster-py-comparer-dev/tests/__init__.py
diff --git a/...ter-py-comparer-dev/tests/test.clustering → ...ter-py-comparer-dev/tests/test.clustering b/...ter-py-comparer-dev/tests/test.clustering → ...ter-py-comparer-dev/tests/test.clustering
diff --git a/...-cluster-py-comparer-dev/tests/test.fasta → ...-cluster-py-comparer-dev/tests/test.fasta b/...-cluster-py-comparer-dev/tests/test.fasta → ...-cluster-py-comparer-dev/tests/test.fasta
diff --git a/...ra-cluster-py-comparer-dev/tests/test.out → ...ra-cluster-py-comparer-dev/tests/test.out b/...ra-cluster-py-comparer-dev/tests/test.out → ...ra-cluster-py-comparer-dev/tests/test.out
diff --git a/...mparer-dev/tests/test_cluster_features.py → ...mparer-dev/tests/test_cluster_features.py b/...mparer-dev/tests/test_cluster_features.py → ...mparer-dev/tests/test_cluster_features.py
diff --git a/...parer-dev/tests/test_clustering_parser.py → ...parer-dev/tests/test_clustering_parser.py b/...parer-dev/tests/test_clustering_parser.py → ...parer-dev/tests/test_clustering_parser.py
diff --git a/...y-comparer-dev/tests/test_fasta_parser.py → ...y-comparer-dev/tests/test_fasta_parser.py b/...y-comparer-dev/tests/test_fasta_parser.py → ...y-comparer-dev/tests/test_fasta_parser.py
diff --git a/...-comparer-dev/tests/test_id_transferer.py → ...-comparer-dev/tests/test_id_transferer.py b/...-comparer-dev/tests/test_id_transferer.py → ...-comparer-dev/tests/test_id_transferer.py
diff --git a/...omparer-dev/tests/test_msamanda_import.py → ...omparer-dev/tests/test_msamanda_import.py b/...omparer-dev/tests/test_msamanda_import.py → ...omparer-dev/tests/test_msamanda_import.py
diff --git a/...parer-dev/tests/test_protein_annotator.py → ...parer-dev/tests/test_protein_annotator.py b/...parer-dev/tests/test_protein_annotator.py → ...parer-dev/tests/test_protein_annotator.py
diff --git a/...omparer-dev/tests/test_scaffold_import.py → ...omparer-dev/tests/test_scaffold_import.py b/...omparer-dev/tests/test_scaffold_import.py → ...omparer-dev/tests/test_scaffold_import.py
diff --git a/...comparer-dev/tests/test_xtandem_import.py → ...comparer-dev/tests/test_xtandem_import.py b/...comparer-dev/tests/test_xtandem_import.py → ...comparer-dev/tests/test_xtandem_import.py
diff --git a/.../tests/testfiles/msamanda_test_output.csv → .../tests/testfiles/msamanda_test_output.csv b/.../tests/testfiles/msamanda_test_output.csv → .../tests/testfiles/msamanda_test_output.csv
diff --git a/.../tests/testfiles/msamanda_test_output.mgf → .../tests/testfiles/msamanda_test_output.mgf b/.../tests/testfiles/msamanda_test_output.mgf → .../tests/testfiles/msamanda_test_output.mgf
diff --git a/...-py-comparer-dev/tests/testfiles/test.mgf → ...-py-comparer-dev/tests/testfiles/test.mgf b/...-py-comparer-dev/tests/testfiles/test.mgf → ...-py-comparer-dev/tests/testfiles/test.mgf
diff --git a/...py-comparer-dev/tests/testfiles/test.mzid → ...py-comparer-dev/tests/testfiles/test.mzid b/...py-comparer-dev/tests/testfiles/test.mzid → ...py-comparer-dev/tests/testfiles/test.mzid
diff --git a/...-py-comparer-dev/tests/testfiles/test.tsv → ...-py-comparer-dev/tests/testfiles/test.tsv b/...-py-comparer-dev/tests/testfiles/test.tsv → ...-py-comparer-dev/tests/testfiles/test.tsv
diff --git a/...rer-dev/tests/testfiles/test_xtandem.mzid → ...rer-dev/tests/testfiles/test_xtandem.mzid b/...rer-dev/tests/testfiles/test_xtandem.mzid → ...rer-dev/tests/testfiles/test_xtandem.mzid
diff --git a/Script1_QC_MGF/Identify_detector.pl → QC_Export_MGF/Identify_detector.pl b/Script1_QC_MGF/Identify_detector.pl → QC_Export_MGF/Identify_detector.pl
diff --git a/Script1_QC_MGF/QC_exporter.sh → QC_Export_MGF/QC_exporter.sh b/Script1_QC_MGF/QC_exporter.sh → QC_Export_MGF/QC_exporter.sh
diff --git a/Script1_QC_MGF/Script_QC_MGF.R → QC_Export_MGF/Script_QC_MGF.R b/Script1_QC_MGF/Script_QC_MGF.R → QC_Export_MGF/Script_QC_MGF.R
diff --git a/Script1_QC_MGF/Script_QC_MGF.Rmd → QC_Export_MGF/Script_QC_MGF.Rmd b/Script1_QC_MGF/Script_QC_MGF.Rmd → QC_Export_MGF/Script_QC_MGF.Rmd
diff --git a/Script1_QC_MGF/Script_QC_MGF.html → QC_Export_MGF/Script_QC_MGF.html b/Script1_QC_MGF/Script_QC_MGF.html → QC_Export_MGF/Script_QC_MGF.html
diff --git a/Script1_QC_MGF/counter.py → QC_Export_MGF/counter.py b/Script1_QC_MGF/counter.py → QC_Export_MGF/counter.py
diff --git a/Script4_QC_Report/QC_cluster_report.R → QC_Peptide_Reports/QC_cluster_report.R b/Script4_QC_Report/QC_cluster_report.R → QC_Peptide_Reports/QC_cluster_report.R
diff --git a/...Report/QC_metrics_for_Peptide_Reports.Rmd → ...eports/QC_metrics_for_Peptide_Reports.Rmd b/...Report/QC_metrics_for_Peptide_Reports.Rmd → ...eports/QC_metrics_for_Peptide_Reports.Rmd
diff --git a/...eport/QC_metrics_for_Peptide_Reports.html → ...ports/QC_metrics_for_Peptide_Reports.html b/...eport/QC_metrics_for_Peptide_Reports.html → ...ports/QC_metrics_for_Peptide_Reports.html
diff --git a/Script4_QC_Report/reporterScript.sh → QC_Peptide_Reports/reporterScript.sh b/Script4_QC_Report/reporterScript.sh → QC_Peptide_Reports/reporterScript.sh