From af37b63f942cf0c6a0ba5f6fe099f71206ac1093 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 31 Jul 2017 15:08:03 +0200 Subject: [PATCH 01/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index adffe39..665e0fa 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -47,7 +47,7 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir): #create sample table if sample2cat is not None: - sample_cat = pd.read_cvs(sample2cat, index_col = 0, sep = "\t") + sample_cat = pd.read_csv(sample2cat, index_col = 0, sep = "\t") #replace index with cleaned file names sample_cat.index.rename(str, dict([(tf, sfn) for sfn, tf in zip(sample_file_names, namelist)])) sample_table = pd.DataFrame([sample_file_names, sample_cat.loc[sample_file_names,]]) From 7938edc0e09b7ac04def5b44ae6bf295041dbbac Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 31 Jul 2017 17:05:40 +0200 Subject: [PATCH 02/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 665e0fa..0328623 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -50,7 +50,8 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir): sample_cat = pd.read_csv(sample2cat, index_col = 0, sep = "\t") #replace index with cleaned file names sample_cat.index.rename(str, dict([(tf, sfn) for sfn, tf in zip(sample_file_names, namelist)])) - sample_table = pd.DataFrame([sample_file_names, sample_cat.loc[sample_file_names,]]) + sample_table = pd.DataFrame([sample_file_names, sample_cat.loc[sample_file_names, ]['category'].tolist()]) + # sample_table = pd.DataFrame([sample_file_names, sample_cat.loc[sample_file_names,]]) sample_table.columns = ["sample_file_name", "category"] else: sample_table = pd.DataFrame(sample_file_names) From 672db82f0452d22a3f07472490e6b27f41aa5197 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 31 Jul 2017 17:31:13 +0200 Subject: [PATCH 03/50] Update traitar_from_archive --- bin/traitar_from_archive | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/bin/traitar_from_archive b/bin/traitar_from_archive index eda8223..1718908 100755 --- a/bin/traitar_from_archive +++ b/bin/traitar_from_archive @@ -14,6 +14,14 @@ if __name__ == "__main__": parser.add_argument("--input_dir", help='directory for the traitar input; will be created if it doesn\'t exist yet', default='traitar_in') parser.add_argument("--output_dir", help='directory for the traitar output; will be created if it doesn\'t exist yet', default='traitar_out') parser.add_argument("--heatmap_format", choices = ["png", "pdf", "svg", "jpg"], default='pdf', help = "choose file format for the heatmap") + + parser.add_argument("--gene_gff_type", default=None) + parser.add_argument("--primary_models", default=None) + parser.add_argument("--secondary_models", default=None) + parser.add_argument("--primary_hmm_db", default=None) + parser.add_argument("--secondary_hmm_db", default=None) + parser.add_argument("--annotation_summary", default=None) + args = parser.parse_args() read_archive(args.input_archive, args.archive_type, args.mode, args.sample2cat, args.input_dir) call_traitar(args) From a9a9b8aa76252bb635977bc3cd9d90b9e01c6f86 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 31 Jul 2017 18:10:06 +0200 Subject: [PATCH 04/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 0328623..74ee9f2 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -50,8 +50,9 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir): sample_cat = pd.read_csv(sample2cat, index_col = 0, sep = "\t") #replace index with cleaned file names sample_cat.index.rename(str, dict([(tf, sfn) for sfn, tf in zip(sample_file_names, namelist)])) - sample_table = pd.DataFrame([sample_file_names, sample_cat.loc[sample_file_names, ]['category'].tolist()]) - # sample_table = pd.DataFrame([sample_file_names, sample_cat.loc[sample_file_names,]]) + sample_table = pd.DataFrame(sample_file_names) + categories = pd.Series(sample_cat.loc[sample_file_names, ]['category'].tolist()) + sample_table['category'] = categories sample_table.columns = ["sample_file_name", "category"] else: sample_table = pd.DataFrame(sample_file_names) From 50577c112d7c942a90dedd104ec0a4bbfa56dc1a Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 31 Jul 2017 19:09:39 +0200 Subject: [PATCH 05/50] Update hmmer2filtered_best.py --- traitar/hmmer2filtered_best.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/hmmer2filtered_best.py b/traitar/hmmer2filtered_best.py index 5e2c6f0..c570a2b 100644 --- a/traitar/hmmer2filtered_best.py +++ b/traitar/hmmer2filtered_best.py @@ -49,7 +49,7 @@ def aggregate_domain_hits(filtered_df, out_f): #sort by gene identifier and Pfam with open(out_f, 'w') as out_fo: ps.DataFrame(filtered_df.columns).T.to_csv(out_f, sep = "\t", index = False, header = False, mode = 'a') - filtered_df.sort_values(by = ["target name", "query name"], inplace = True) + filtered_df.sort_index(by = ["target name", "query name"], inplace = True) if filtered_df.shape[0] > 0: current_max = filtered_df.iloc[0,] else: From 762e9e53608225f70862a635b218b7e82af5aa7b Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 31 Jul 2017 20:52:23 +0200 Subject: [PATCH 06/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 74ee9f2..d1e7a0d 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -70,3 +70,8 @@ def call_traitar(args): #compress output with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) + + # test case + args.out2_archive = "dialign_output_aaalignment2.FILE" + with tarfile.open(args.out2_archive, "w:gz") as tar: + tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) From d98f8081550e0965816626979cd4592fa7d38fcc Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 1 Aug 2017 10:57:48 +0200 Subject: [PATCH 07/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index d1e7a0d..8c8a274 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -4,6 +4,8 @@ import re import os from .traitar import phenolyze +from shutil import copyfile + def get_sample_names(namelist): """parse sample names""" @@ -70,8 +72,5 @@ def call_traitar(args): #compress output with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - - # test case - args.out2_archive = "dialign_output_aaalignment2.FILE" - with tarfile.open(args.out2_archive, "w:gz") as tar: - tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) + + copyfile(args.output_dir+"/traitar_out/phenotype_prediction/heatmap_combined.pdf", args.out_image) From aef82e11d27c51cdc1db3fc0eda260647d9b30b2 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 1 Aug 2017 11:00:49 +0200 Subject: [PATCH 08/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 8c8a274..47b9a0a 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -73,4 +73,5 @@ def call_traitar(args): with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - copyfile(args.output_dir+"/traitar_out/phenotype_prediction/heatmap_combined.pdf", args.out_image) + out_image = args.out_archive.replace('.FILE', '2.FILE') + copyfile(args.output_dir+"/traitar_out/phenotype_prediction/heatmap_combined.pdf", out_image) From 3e22f3e99f5f8f7eb4e8e36aa862fc4d3d8a7615 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 1 Aug 2017 11:28:40 +0200 Subject: [PATCH 09/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 47b9a0a..b457196 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -74,4 +74,4 @@ def call_traitar(args): tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) out_image = args.out_archive.replace('.FILE', '2.FILE') - copyfile(args.output_dir+"/traitar_out/phenotype_prediction/heatmap_combined.pdf", out_image) + copyfile(args.output_dir+"/phenotype_prediction/heatmap_combined.pdf", out_image) From d3e6c2cab0c074d7b753f06ad7e1310b2e93fe40 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 7 Aug 2017 16:12:47 +0200 Subject: [PATCH 10/50] Update traitar.py --- traitar/traitar.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/traitar/traitar.py b/traitar/traitar.py index 863770e..9ff10be 100644 --- a/traitar/traitar.py +++ b/traitar/traitar.py @@ -243,7 +243,8 @@ def execute_commands(self, commands, joblog = None): if self.cpu > 1: #run with parallel #ps.DataFrame(commands).to_csv(tf, index = False, header = False) - p = Popen("parallel --will-cite %s -j %s" % ("--joblog %s" % joblog if joblog is not None else "", self.cpu), stdout = devnull, shell = True, executable = "/bin/bash", stdin = PIPE, env = env) + # p = Popen("parallel --will-cite %s -j %s" % ("--joblog %s" % joblog if joblog is not None else "", self.cpu), stdout = devnull, shell = True, executable = "/bin/bash", stdin = PIPE, env = env) + p = Popen("parallel %s -j %s" % ("--joblog %s" % joblog if joblog is not None else "", self.cpu), stdout = devnull, shell = True, executable = "/bin/bash", stdin = PIPE, env = env) p.communicate(input = "\n".join(commands)) if p.returncode != 0: if not joblog is None: From a62ddc9a544670e88ca9e44ec887e617840ad611 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 7 Aug 2017 16:41:29 +0200 Subject: [PATCH 11/50] Update hmm2gff.py --- traitar/hmm2gff.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/hmm2gff.py b/traitar/hmm2gff.py index ec7727b..69a6a5a 100644 --- a/traitar/hmm2gff.py +++ b/traitar/hmm2gff.py @@ -227,7 +227,7 @@ def write_hmm_gff(hmmer_file, out_gff_dir, gene_dict, sample, skip_genes, mode, if not len(out_table) == 0: out_table_df = ps.read_csv(StringIO.StringIO("".join(out_table)), sep = "\t", header = None) out_table_df.columns = ["Phenotype", "gene_id", "acc", "description", "cor"] - out_table_df.sort(columns = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) + out_table_df.sort_values(columns = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) #close out gffs if not gene_dict is None: for i in out_gffs: From 3adb0c6bf6fe5c429963785306eb07de5d50c3a6 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 7 Aug 2017 16:49:51 +0200 Subject: [PATCH 12/50] Update hmm2gff.py --- traitar/hmm2gff.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/traitar/hmm2gff.py b/traitar/hmm2gff.py index 69a6a5a..50317b5 100644 --- a/traitar/hmm2gff.py +++ b/traitar/hmm2gff.py @@ -227,7 +227,8 @@ def write_hmm_gff(hmmer_file, out_gff_dir, gene_dict, sample, skip_genes, mode, if not len(out_table) == 0: out_table_df = ps.read_csv(StringIO.StringIO("".join(out_table)), sep = "\t", header = None) out_table_df.columns = ["Phenotype", "gene_id", "acc", "description", "cor"] - out_table_df.sort_values(columns = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) + # out_table_df.sort_values(columns = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) + out_table_df.sort_values(by = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) #close out gffs if not gene_dict is None: for i in out_gffs: From 3e895942616ca770d3ebcde1ef0a8230cf251f66 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 8 Aug 2017 12:29:57 +0200 Subject: [PATCH 13/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index b457196..37a44ee 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -36,7 +36,7 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir): archive = zipfile.open(input_archive) namelist = archive.namelist() if archive_type == "tar.gz": - archive = tarfile.open(input_archive, "r:gz") + archive = tarfile.open(input_archive, "r") namelist = archive.getnames() sample_file_names, sample_names = get_sample_names(namelist) for tf, sfn in zip(namelist, sample_file_names): From 66f9cb473c61bc1d33f36f6de2038038e292552f Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 8 Aug 2017 14:06:39 +0200 Subject: [PATCH 14/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 37a44ee..a6bd411 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -73,5 +73,5 @@ def call_traitar(args): with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - out_image = args.out_archive.replace('.FILE', '2.FILE') - copyfile(args.output_dir+"/phenotype_prediction/heatmap_combined.pdf", out_image) + if args.out_image is not None: + copyfile(args.output_dir+"/phenotype_prediction/heatmap_combined.pdf", out_image) From 570b0e99864c9c0afca886c31d28bf9d4d880213 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 8 Aug 2017 14:07:38 +0200 Subject: [PATCH 15/50] Update traitar_from_archive --- bin/traitar_from_archive | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/traitar_from_archive b/bin/traitar_from_archive index 1718908..542a182 100755 --- a/bin/traitar_from_archive +++ b/bin/traitar_from_archive @@ -21,6 +21,7 @@ if __name__ == "__main__": parser.add_argument("--primary_hmm_db", default=None) parser.add_argument("--secondary_hmm_db", default=None) parser.add_argument("--annotation_summary", default=None) + parser.add_argument("--output_image", default=None) args = parser.parse_args() read_archive(args.input_archive, args.archive_type, args.mode, args.sample2cat, args.input_dir) From c912740c97a1c717199682a8101e268824e20d42 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 8 Aug 2017 14:27:47 +0200 Subject: [PATCH 16/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index a6bd411..6d55b69 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -73,5 +73,5 @@ def call_traitar(args): with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - if args.out_image is not None: - copyfile(args.output_dir+"/phenotype_prediction/heatmap_combined.pdf", out_image) + if args.output_image is not None: + copyfile(args.output_dir+"/phenotype_prediction/heatmap_combined.pdf", output_image) From 6bc5cf0da9a0b1f305b62268860b3ca76452de13 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 8 Aug 2017 14:36:01 +0200 Subject: [PATCH 17/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 6d55b69..00c6f0b 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -74,4 +74,4 @@ def call_traitar(args): tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) if args.output_image is not None: - copyfile(args.output_dir+"/phenotype_prediction/heatmap_combined.pdf", output_image) + copyfile(args.output_dir+"/phenotype_prediction/heatmap_combined.pdf", args.output_image) From 16bba58ad14e13bda91feed005ca58d95ff62894 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 8 Aug 2017 15:34:52 +0200 Subject: [PATCH 18/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 00c6f0b..4bd51a4 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -74,4 +74,5 @@ def call_traitar(args): tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) if args.output_image is not None: - copyfile(args.output_dir+"/phenotype_prediction/heatmap_combined.pdf", args.output_image) + image_source = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format + copyfile(image_source, args.output_image) From aa0f57c68b93b2643d433aa24616f398adf27f5f Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Thu, 17 Aug 2017 14:26:19 +0200 Subject: [PATCH 19/50] Update hmm2gff.py --- traitar/hmm2gff.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/traitar/hmm2gff.py b/traitar/hmm2gff.py index 50317b5..30a4995 100644 --- a/traitar/hmm2gff.py +++ b/traitar/hmm2gff.py @@ -228,7 +228,8 @@ def write_hmm_gff(hmmer_file, out_gff_dir, gene_dict, sample, skip_genes, mode, out_table_df = ps.read_csv(StringIO.StringIO("".join(out_table)), sep = "\t", header = None) out_table_df.columns = ["Phenotype", "gene_id", "acc", "description", "cor"] # out_table_df.sort_values(columns = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) - out_table_df.sort_values(by = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) + # out_table_df.sort_values(by = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) + out_table_df.sort(columns = ["Phenotype", "cor"], ascending = [True, False]).to_csv("%s/%s_important_features.dat" % (out_gff_dir, sample), sep = "\t", index = None) #close out gffs if not gene_dict is None: for i in out_gffs: From 32feba07ab9a69fd386a7e47c6736fc2c5e16501 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Thu, 21 Sep 2017 02:44:56 +0200 Subject: [PATCH 20/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 4bd51a4..a02a983 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -75,4 +75,4 @@ def call_traitar(args): if args.output_image is not None: image_source = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format - copyfile(image_source, args.output_image) + copyfile(image_source, os.path.dirname(args.out_archive)+'/'+args.output_image) From d14774d892a9637745506f617959452add1b4fbb Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 9 Oct 2017 14:07:07 +0200 Subject: [PATCH 21/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index a02a983..4bd51a4 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -75,4 +75,4 @@ def call_traitar(args): if args.output_image is not None: image_source = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format - copyfile(image_source, os.path.dirname(args.out_archive)+'/'+args.output_image) + copyfile(image_source, args.output_image) From 7889c1c4330afa634a2cade550ab34e467739888 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 9 Oct 2017 14:10:11 +0200 Subject: [PATCH 22/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 4bd51a4..6abcba5 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -75,4 +75,9 @@ def call_traitar(args): if args.output_image is not None: image_source = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format - copyfile(image_source, args.output_image) + if args.output_image[0] == '/': + output_image = args.output_image + else: + output_image = os.path.dirname(args.out_archive)+'/'+args.output_image + + copyfile(image_source, output_image) From 0da17a752288d9564f36413d0980891f0bc3c607 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 9 Oct 2017 14:23:55 +0200 Subject: [PATCH 23/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 6abcba5..d3fc0de 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -75,7 +75,7 @@ def call_traitar(args): if args.output_image is not None: image_source = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format - if args.output_image[0] == '/': + if args.output_image[0:1] == '/': output_image = args.output_image else: output_image = os.path.dirname(args.out_archive)+'/'+args.output_image From 9de46331b199030ea4955c1e2a5a3ccd58875ffe Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 10 Oct 2017 16:18:50 +0200 Subject: [PATCH 24/50] Update traitar_from_archive --- bin/traitar_from_archive | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/traitar_from_archive b/bin/traitar_from_archive index 542a182..25328e5 100755 --- a/bin/traitar_from_archive +++ b/bin/traitar_from_archive @@ -22,6 +22,7 @@ if __name__ == "__main__": parser.add_argument("--secondary_hmm_db", default=None) parser.add_argument("--annotation_summary", default=None) parser.add_argument("--output_image", default=None) + parser.add_argument("--generate_galaxy_html", default=None) args = parser.parse_args() read_archive(args.input_archive, args.archive_type, args.mode, args.sample2cat, args.input_dir) From 5342e892e3fa684c8d1e8797e4655eddf75dd74a Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 10 Oct 2017 16:30:50 +0200 Subject: [PATCH 25/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index d3fc0de..bed45e6 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -70,14 +70,21 @@ def call_traitar(args): args.sample2file = "%s/sample_table.txt" % args.input_dir phenolyze(args) #compress output - with tarfile.open(args.out_archive, "w:gz") as tar: - tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) + + if args.generate_galaxy_html is not None: + # create html dir + # copy our image there + # create our tar file there + # copy our sample html to html file + else: + with tarfile.open(args.out_archive, "w:gz") as tar: + tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - if args.output_image is not None: - image_source = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format - if args.output_image[0:1] == '/': - output_image = args.output_image - else: - output_image = os.path.dirname(args.out_archive)+'/'+args.output_image + if args.output_image is not None: + image_source = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format + if args.output_image[0:1] == '/': + output_image = args.output_image + else: + output_image = os.path.dirname(args.out_archive)+'/'+args.output_image - copyfile(image_source, output_image) + copyfile(image_source, output_image) From a3342a52e94e01fc7fb8d3beb12447b7d7e7ee2d Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 10 Oct 2017 17:00:36 +0200 Subject: [PATCH 26/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index bed45e6..9d7da61 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -72,10 +72,13 @@ def call_traitar(args): #compress output if args.generate_galaxy_html is not None: - # create html dir - # copy our image there - # create our tar file there - # copy our sample html to html file + (html_file, html_dir) = args.generate_galaxy_html. split(':') + os.makedirs(html_dir) + image_name = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format + copyfile(image_name, html_dir) + with tarfile.open(html_dir+"/archive.tar.gz", "w:gz") as tar: + tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) + copyfile(sample_html, html_dir) else: with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) From e25d8ad224901a45a3879d60a4652017485a7496 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 16 Oct 2017 16:52:47 +0200 Subject: [PATCH 27/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 34 +++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 14 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 9d7da61..3ccbcee 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -3,6 +3,7 @@ import pandas as pd import re import os +import os.path from .traitar import phenolyze from shutil import copyfile @@ -32,20 +33,25 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir): """read archive""" if not os.path.exists(input_dir): os.mkdir(input_dir) - if archive_type == "zip": - archive = zipfile.open(input_archive) - namelist = archive.namelist() - if archive_type == "tar.gz": - archive = tarfile.open(input_archive, "r") - namelist = archive.getnames() - sample_file_names, sample_names = get_sample_names(namelist) - for tf, sfn in zip(namelist, sample_file_names): - extracted = archive.extractfile(tf) - with open("%s/%s" % (input_dir, sfn), 'w') as sample_file_out: - for line in extracted: - sample_file_out.write(line) - extracted.close() - + + if archive_type == "zip" or archive_type == "tar.gz": + if archive_type == "zip": + archive = zipfile.open(input_archive) + namelist = archive.namelist() + if archive_type == "tar.gz": + archive = tarfile.open(input_archive, "r") + namelist = archive.getnames() + sample_file_names, sample_names = get_sample_names(namelist) + for tf, sfn in zip(namelist, sample_file_names): + extracted = archive.extractfile(tf) + with open("%s/%s" % (input_dir, sfn), 'w') as sample_file_out: + for line in extracted: + sample_file_out.write(line) + extracted.close() + elif archive_type == "directory": + for input_part in input_archive.split(','): + input_dir_part=os.path.basename(input_part) + os.symlink(input_part, input_dir+"/"+input_dir_part) #create sample table if sample2cat is not None: From cf1ec36a7fa680cfb2fbfa88f1644a7323160f4a Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 09:34:12 +0200 Subject: [PATCH 28/50] Create sample.html --- traitar/html/sample.html | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 traitar/html/sample.html diff --git a/traitar/html/sample.html b/traitar/html/sample.html new file mode 100644 index 0000000..2af4fa5 --- /dev/null +++ b/traitar/html/sample.html @@ -0,0 +1,9 @@ + + + + +

My First Heading

+

My first paragraph.

+ + + From 5d21ce81d446fc2e82205fc04b52e7f8bf320169 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 09:48:22 +0200 Subject: [PATCH 29/50] Update sample.html --- traitar/html/sample.html | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/traitar/html/sample.html b/traitar/html/sample.html index 2af4fa5..37df110 100644 --- a/traitar/html/sample.html +++ b/traitar/html/sample.html @@ -2,8 +2,9 @@ -

My First Heading

-

My first paragraph.

+ archive.tar.gz + + From 2b79d38815a884869b755fc40291fbee2136f758 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 09:49:39 +0200 Subject: [PATCH 30/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 3ccbcee..e8a1c91 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -84,7 +84,7 @@ def call_traitar(args): copyfile(image_name, html_dir) with tarfile.open(html_dir+"/archive.tar.gz", "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - copyfile(sample_html, html_dir) + copyfile('html/sample.html', html_dir) else: with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) From c4a2cea6fdad250e6e2576c4f2072a3aa25d3794 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 11:08:50 +0200 Subject: [PATCH 31/50] Update traitar_from_archive --- bin/traitar_from_archive | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/traitar_from_archive b/bin/traitar_from_archive index 25328e5..2dd4c21 100755 --- a/bin/traitar_from_archive +++ b/bin/traitar_from_archive @@ -6,7 +6,7 @@ if __name__ == "__main__": import argparse parser = argparse.ArgumentParser("Traitar wrapper") parser.add_argument("input_archive", help='directory with the input data') - parser.add_argument("archive_type", help='specify kind of archive', choices = ["tar.gz", "zip"]) + parser.add_argument("archive_type", help='specify kind of archive', choices = ["tar.gz", "zip", "directory"]) parser.add_argument("mode", help='either from_genes if gene prediction amino acid fasta is available in input_dir otherwise from_nucleotides in this case Prodigal is used to determine the ORFs from the nucleotide fasta files in input_dir', choices=["from_genes", "from_nucleotides", "from_annotation_summary"]) parser.add_argument("out_archive", help='compressed traitar output foldder') parser.add_argument("-c", "--cpus", help='number of cpus used for the individual steps; maximum is number of samples; needs parallel', default = 1) From 40ffc2f594a540fd75187f4c3b00fb219e7d4e3f Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 11:11:24 +0200 Subject: [PATCH 32/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index e8a1c91..b848abd 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -84,7 +84,7 @@ def call_traitar(args): copyfile(image_name, html_dir) with tarfile.open(html_dir+"/archive.tar.gz", "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - copyfile('html/sample.html', html_dir) + copyfile('html/sample.html', html_file) else: with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) From 1fb8045c09b42e0143713ea66ada58fbe8e93e3b Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 11:44:37 +0200 Subject: [PATCH 33/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index b848abd..037d225 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -49,9 +49,13 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir): sample_file_out.write(line) extracted.close() elif archive_type == "directory": + namelist = [] for input_part in input_archive.split(','): input_dir_part=os.path.basename(input_part) + namelist.append([input_dir_part]) os.symlink(input_part, input_dir+"/"+input_dir_part) + sample_file_names, sample_names = get_sample_names(namelist) + #create sample table if sample2cat is not None: From cca8e3a492d0d4638e56eaf06be39949a0cc7607 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 17:08:01 +0200 Subject: [PATCH 34/50] Update traitar_from_archive --- bin/traitar_from_archive | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/traitar_from_archive b/bin/traitar_from_archive index 2dd4c21..5d54e66 100755 --- a/bin/traitar_from_archive +++ b/bin/traitar_from_archive @@ -23,6 +23,7 @@ if __name__ == "__main__": parser.add_argument("--annotation_summary", default=None) parser.add_argument("--output_image", default=None) parser.add_argument("--generate_galaxy_html", default=None) + parser.add_argument("--input_names", default=None) args = parser.parse_args() read_archive(args.input_archive, args.archive_type, args.mode, args.sample2cat, args.input_dir) From 632179efa294489a4584610bf10b862b6a077234 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 17:10:14 +0200 Subject: [PATCH 35/50] Update traitar_from_archive --- bin/traitar_from_archive | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/traitar_from_archive b/bin/traitar_from_archive index 5d54e66..d6138b0 100755 --- a/bin/traitar_from_archive +++ b/bin/traitar_from_archive @@ -26,6 +26,6 @@ if __name__ == "__main__": parser.add_argument("--input_names", default=None) args = parser.parse_args() - read_archive(args.input_archive, args.archive_type, args.mode, args.sample2cat, args.input_dir) + read_archive(args.input_archive, args.archive_type, args.mode, args.sample2cat, args.input_dir, args.input_names) call_traitar(args) From 1582fc697649d3f87349c93cfe317d5a9547342c Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 17 Oct 2017 17:12:49 +0200 Subject: [PATCH 36/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 037d225..3ec0a7d 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -29,7 +29,7 @@ def get_sample_names(namelist): -def read_archive(input_archive, archive_type, mode, sample2cat, input_dir): +def read_archive(input_archive, archive_type, mode, sample2cat, input_dir, input_names): """read archive""" if not os.path.exists(input_dir): os.mkdir(input_dir) @@ -49,7 +49,7 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir): sample_file_out.write(line) extracted.close() elif archive_type == "directory": - namelist = [] + namelist = input_names.split(',') for input_part in input_archive.split(','): input_dir_part=os.path.basename(input_part) namelist.append([input_dir_part]) From fb46973d637bf97d4fc6a198281fb09bcaece6d8 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Wed, 18 Oct 2017 10:09:36 +0200 Subject: [PATCH 37/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 3ec0a7d..e1ca463 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -49,19 +49,19 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir, input sample_file_out.write(line) extracted.close() elif archive_type == "directory": - namelist = input_names.split(',') + sample_names = input_names.split(',') for input_part in input_archive.split(','): input_dir_part=os.path.basename(input_part) - namelist.append([input_dir_part]) + sample_file_names.append(input_dir_part) os.symlink(input_part, input_dir+"/"+input_dir_part) - sample_file_names, sample_names = get_sample_names(namelist) #create sample table if sample2cat is not None: sample_cat = pd.read_csv(sample2cat, index_col = 0, sep = "\t") #replace index with cleaned file names - sample_cat.index.rename(str, dict([(tf, sfn) for sfn, tf in zip(sample_file_names, namelist)])) + if archive_type != "directory": + sample_cat.index.rename(str, dict([(tf, sfn) for sfn, tf in zip(sample_file_names, namelist)])) sample_table = pd.DataFrame(sample_file_names) categories = pd.Series(sample_cat.loc[sample_file_names, ]['category'].tolist()) sample_table['category'] = categories From c6b2dd7a9a22c41ce541597e380658a28bf0a5f4 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Wed, 18 Oct 2017 10:44:11 +0200 Subject: [PATCH 38/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 1 + 1 file changed, 1 insertion(+) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index e1ca463..35239ee 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -50,6 +50,7 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir, input extracted.close() elif archive_type == "directory": sample_names = input_names.split(',') + sample_file_names = [] for input_part in input_archive.split(','): input_dir_part=os.path.basename(input_part) sample_file_names.append(input_dir_part) From 872502c379dabf61d44686f5b792d34faece892a Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Wed, 18 Oct 2017 11:06:31 +0200 Subject: [PATCH 39/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 35239ee..2f85dff 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -63,8 +63,11 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir, input #replace index with cleaned file names if archive_type != "directory": sample_cat.index.rename(str, dict([(tf, sfn) for sfn, tf in zip(sample_file_names, namelist)])) - sample_table = pd.DataFrame(sample_file_names) - categories = pd.Series(sample_cat.loc[sample_file_names, ]['category'].tolist()) + sample_table = pd.DataFrame(sample_file_names) + categories = pd.Series(sample_cat.loc[sample_file_names, ]['category'].tolist()) + else: + sample_table = pd.DataFrame(sample_names) + categories = pd.Series(sample_cat.loc[sample_names, ]['category'].tolist()) sample_table['category'] = categories sample_table.columns = ["sample_file_name", "category"] else: From af9ae876d4f1931bf49d064a729b8392f2fca0b9 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Wed, 18 Oct 2017 14:59:10 +0200 Subject: [PATCH 40/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 2f85dff..dd3f1cf 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -63,10 +63,10 @@ def read_archive(input_archive, archive_type, mode, sample2cat, input_dir, input #replace index with cleaned file names if archive_type != "directory": sample_cat.index.rename(str, dict([(tf, sfn) for sfn, tf in zip(sample_file_names, namelist)])) - sample_table = pd.DataFrame(sample_file_names) + sample_table = pd.DataFrame(sample_names) categories = pd.Series(sample_cat.loc[sample_file_names, ]['category'].tolist()) else: - sample_table = pd.DataFrame(sample_names) + sample_table = pd.DataFrame(sample_file_names) categories = pd.Series(sample_cat.loc[sample_names, ]['category'].tolist()) sample_table['category'] = categories sample_table.columns = ["sample_file_name", "category"] From 940d143b7f6d02a01e7be0632bc046a2fb4cd6d2 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Wed, 18 Oct 2017 15:37:04 +0200 Subject: [PATCH 41/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index dd3f1cf..45ee08c 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -86,13 +86,13 @@ def call_traitar(args): #compress output if args.generate_galaxy_html is not None: - (html_file, html_dir) = args.generate_galaxy_html. split(':') + (html_file, html_dir) = args.generate_galaxy_html.split(':') os.makedirs(html_dir) image_name = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format copyfile(image_name, html_dir) with tarfile.open(html_dir+"/archive.tar.gz", "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - copyfile('html/sample.html', html_file) + copyfile('/home/traitar/traitar/html/sample.html', html_file) else: with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) From 61b3fa5e980c2dfde8c62df112ec5899afd3bc93 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Wed, 18 Oct 2017 17:22:33 +0200 Subject: [PATCH 42/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 45ee08c..0918d17 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -89,7 +89,8 @@ def call_traitar(args): (html_file, html_dir) = args.generate_galaxy_html.split(':') os.makedirs(html_dir) image_name = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format - copyfile(image_name, html_dir) + target_image_name = html_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format + copyfile(image_name, target_image_name) with tarfile.open(html_dir+"/archive.tar.gz", "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) copyfile('/home/traitar/traitar/html/sample.html', html_file) From ecd6c75dc749b7602315c24468d6c910b1ab03fc Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Thu, 19 Oct 2017 15:33:06 +0200 Subject: [PATCH 43/50] Update traitar_from_archive.py --- traitar/traitar_from_archive.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/traitar/traitar_from_archive.py b/traitar/traitar_from_archive.py index 0918d17..bbbc4a2 100644 --- a/traitar/traitar_from_archive.py +++ b/traitar/traitar_from_archive.py @@ -89,11 +89,11 @@ def call_traitar(args): (html_file, html_dir) = args.generate_galaxy_html.split(':') os.makedirs(html_dir) image_name = args.output_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format - target_image_name = html_dir+"/phenotype_prediction/heatmap_combined.%s" % args.heatmap_format + target_image_name = html_dir+"/heatmap_combined.%s" % args.heatmap_format copyfile(image_name, target_image_name) with tarfile.open(html_dir+"/archive.tar.gz", "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) - copyfile('/home/traitar/traitar/html/sample.html', html_file) + copyfile('/home/traitar/traitar/traitar/html/sample.html', html_file) else: with tarfile.open(args.out_archive, "w:gz") as tar: tar.add(args.output_dir, arcname=os.path.basename(args.output_dir)) From e99511efe1732fe44b9791d22d997511bdb9509f Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 7 Nov 2017 11:10:16 +0100 Subject: [PATCH 44/50] Update sample.html --- traitar/html/sample.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/html/sample.html b/traitar/html/sample.html index 37df110..8fa5aef 100644 --- a/traitar/html/sample.html +++ b/traitar/html/sample.html @@ -3,7 +3,7 @@ archive.tar.gz - + From 5b3f68245df8772a1d5d778e5218fa8c0d02fe60 Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 7 Nov 2017 11:57:58 +0100 Subject: [PATCH 45/50] Update sample.html --- traitar/html/sample.html | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/traitar/html/sample.html b/traitar/html/sample.html index 8fa5aef..5895ffe 100644 --- a/traitar/html/sample.html +++ b/traitar/html/sample.html @@ -1,10 +1,13 @@ - - archive.tar.gz - + + + +An archive containing the complete output can be downloaded here. +
+Submit another Traitar job From f94d4baf5d958c00923643370115e364f708444d Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Tue, 7 Nov 2017 11:58:31 +0100 Subject: [PATCH 46/50] Add files via upload --- traitar/html/traitar.png | Bin 0 -> 9981 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 traitar/html/traitar.png diff --git a/traitar/html/traitar.png b/traitar/html/traitar.png new file mode 100644 index 0000000000000000000000000000000000000000..7fb69dedca3797be68059837f2a5a13e2cc2b733 GIT binary patch literal 9981 zcmV00004b3#c}2nYxW zd ze4nF039tv)>-)ReZnqz7*Uq2D5U08W?S-tYENg6R>@+FmPk_ll*E&Uxpa@e2R0W*3 z0LcL#Q;6!10^b1Zgb<(Vy8hXW88e)beugsv9iC7Qha*`^d9M)SR-lXT^e*6Y;BzVE zCSBKe&YU^(cvE#rDaF#IOH*}S?<1w`Bc(hW7zvC31_7F{s23;zJ_7PwF4x-GvuEp( zezwyQ9hOi91qGI(qN0a^`v4no7pryt1;r`rvRl zVucWw8-|f4gh&T^_%0m-vV;(?rKhK_Zm<5d7djlFva_>?Ynrwkr6YZ;Y1++cX=(dU zWuK&!V#$&v6Qq>a0<)>r-!=mag%FF=)6>gNT@NFN4n?S(oSd_T5MQBmrNu6n>*mu< zcgfGsH#?oqsX~Z(KssOss)Z1*3nBiPmX@~T6nC*z=rDxJ%E~gu#>RdsrJMx3S6Enh zO=f1MajN^(81nM+dg;182bc$R2Mpj{;3>P^zV4KEu7&6@gmO3>bAbiGey`U%BAi*< z>4LnxyePvkekP^-6)*shfWt71-_4jYW5X%#UbE042$h+csf`{zdMhwU2ysh#diqPJ zx=$@ZR#uiNIy(AlA;j;2VJL}}rD@tDXUb66AqbV7ojpm@w3R@q$z!HnL6vb9PC(3{MYTH>Dbe z)>YSu*LAE?5(QX&_tgMyA#ejHG>s!>GbJXIQLJfRr>0o}LxVycvVoih3l?ky$j!}7 zlu~8_cc5m4pK6*m?{pjnI|`vz08@kzx2C73FKDZFX3d&q>fE{Wk4=zi2r(c<*FERC z-Iie<52SNu*+g$kHsRlo6VjIO|zP$EcC+j)z#H+z542_mASdO=SnFT0pn4o zhR0J=Q~z(wm@%G+JYWRSQ3&-Ja1n5`-EM!mE!vnnckVC~ykQ72yua70U+Qw1`gy%= z(G(KcWwG!@RFtvZY!;djl?FUsR#x`xtXZ@4=;-Ksg%FPcF;dC`Ddn{@X3W^tCY@;} zw5E%k{*Y20@f~(+i~4W9_0}1h5Ct|Vhs~*|;AW?@&Bz4mEg$Ida6?6fc3*k980mJ~ zkn-s+iHVz*FJC@6BO~Ka!1=&eLWnV%rWNMoHbLRBYgm@!G*R>m+ zPAyJ0J+V4qHuGAiBsRxg%_iG*ykkq|8*AgF@(4kh$%IEVtbz2=yp<|)|(IE(BHk&_1sUCwJ4oA;O)vIaR zZ>5y+vnngKs4&O`@MTmqF3Tv~mf?8K193)8;j1WHgXMQxEIgf%%s&$P@kBy0Uq;0= zSXKa+xm;XRS&5Kxn#b*4I&a>*Si9Yxr)k;+z;@tLi^a0W=aJg(=n#aOHf>swl=5>x z2qAtNi8|-an`Z%j+Ry8yM>A${U349jQF`*b#W+m741K>>2;PW`=UD8IDYD&5sqIdd z#KuzIh@=7-;db+*iVDpzjPbzV0MgRZb_gLRpq%>p1D|GRXO9fK;}JrKAQXTQ;uQcX z<&Bw{nXP^FH%Imn#kU571T9w2yOhb0;?I0a}R;Lnz=a zQ~<%?F=NKeZf#|nro{k6hdI>w5o;LSTYik|o!hy-d?UX)ag;T3sEvPS(M3O(Q!lk?%}qk_<01 zD~~tJNc!K{SiX*mGQ7H;^5TmxmIhwS$;tVv5aJg=sitX{wuS3+U34S~1@Hp!9Wbb( zqT=4xRJ3T(qJ07m?zCFlbj_@@Vem8OF&;i%!tLe9nr(6Ksq0A4EEda`!9io zK$2k?OC1hJp9pokL3AiW+3of!DdkL)ygKTmG7FcIW-4IHT5r)QXU9(Ju@@Yuv)D* z0vmu4ZnyhoDP^0fIvq-f^26b9Bm-Xqy?`g|cKh#ITGws2-FB%ojO7D79@9@NDug+V zduoJWna#$=s3>$H=#r2?Cz}ngu2b!HbF8e4YLACxvzZ~4l?->g>E42+90T}kLV|JJ zWZL(_zy8&~v9dmY`vM?IN_ksGM#jII-C!8#kc0woI2;!O`G6*+oRN`{k=xR`=FXja zqb9_Qy}e#}U1g=o*1)XIk9XtZ*qfZp^*7wW;B(GF)9McdWo2dT+rOVRt5>se>sE%l z-Au2jAf_3!%GJ@)EQyIhN_pqPg$ti=s(emP&b2~_H-JjRFh;b+f^vr&^8B#d?JK2} z4*;4F;y*b#Ib&N|*TRJhUooUi|ITc#`g^BN`d)M6aw^&|&~+V~%@&eO0Evl-j2tn7 z+wQo7haY-~L#e6c+8VZ~*Tp`wnGa)P45VDyvuDp2!nr3SBjZh!J{6~F+QP6KYX&+j zp#U;6GX5&1d=`ikLOAmB@){i$8pFbc3qR1M9OKfoZHqc};?1}?S=Inqu5h^+Sz5{; 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-Submit another Traitar job - +To submit another Traitar job, use the links on the left-hand pane of this window. +
+ From 9c1f6439703ccf4a17f21375f0a8445bc788570c Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Sat, 6 Jan 2018 00:37:38 +0100 Subject: [PATCH 49/50] Update sample.html --- traitar/html/sample.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/traitar/html/sample.html b/traitar/html/sample.html index 0201abf..12cffde 100644 --- a/traitar/html/sample.html +++ b/traitar/html/sample.html @@ -9,6 +9,6 @@
To submit another Traitar job, use the links on the left-hand pane of this window.
- + From 18f96c3303d73038b8d89f66118e51842effb08e Mon Sep 17 00:00:00 2001 From: Gary Robertson Date: Mon, 3 Apr 2023 19:00:55 +0200 Subject: [PATCH 50/50] Post merge changes --- traitar/hmmer2filtered_best.py | 2 +- traitar/traitar.py | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/traitar/hmmer2filtered_best.py b/traitar/hmmer2filtered_best.py index c570a2b..a1fe4a7 100644 --- a/traitar/hmmer2filtered_best.py +++ b/traitar/hmmer2filtered_best.py @@ -49,7 +49,7 @@ def aggregate_domain_hits(filtered_df, out_f): #sort by gene identifier and Pfam with open(out_f, 'w') as out_fo: ps.DataFrame(filtered_df.columns).T.to_csv(out_f, sep = "\t", index = False, header = False, mode = 'a') - filtered_df.sort_index(by = ["target name", "query name"], inplace = True) + filtered_df.sort_values(by = ["target name", "query name"], inplace = True) # index if filtered_df.shape[0] > 0: current_max = filtered_df.iloc[0,] else: diff --git a/traitar/traitar.py b/traitar/traitar.py index 9ff10be..d574ec7 100644 --- a/traitar/traitar.py +++ b/traitar/traitar.py @@ -243,8 +243,7 @@ def execute_commands(self, commands, joblog = None): if self.cpu > 1: #run with parallel #ps.DataFrame(commands).to_csv(tf, index = False, header = False) - # p = Popen("parallel --will-cite %s -j %s" % ("--joblog %s" % joblog if joblog is not None else "", self.cpu), stdout = devnull, shell = True, executable = "/bin/bash", stdin = PIPE, env = env) - p = Popen("parallel %s -j %s" % ("--joblog %s" % joblog if joblog is not None else "", self.cpu), stdout = devnull, shell = True, executable = "/bin/bash", stdin = PIPE, env = env) + p = Popen("parallel --will-cite %s -j %s" % ("--joblog %s" % joblog if joblog is not None else "", self.cpu), stdout = devnull, shell = True, executable = "/bin/bash", stdin = PIPE, env = env) p.communicate(input = "\n".join(commands)) if p.returncode != 0: if not joblog is None: