From 56d06d90e8590789ea718446ff11835dafc3d8f6 Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Tue, 19 Sep 2023 14:40:05 -0700 Subject: [PATCH] Bump HIVIntact from 1.3 to 1.4 --- Pipfile | 2 +- Pipfile.lock | 224 ++++++++++++++++++++++-------------------- Singularity | 2 +- gene_splicer/utils.py | 42 ++++---- setup.py | 2 +- 5 files changed, 142 insertions(+), 130 deletions(-) diff --git a/Pipfile b/Pipfile index 80785b2..bd1ed10 100644 --- a/Pipfile +++ b/Pipfile @@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0" pandas = "==2.0.2" requests = "==2.31.0" pyyaml = "*" -intactness-pipeline = {ref = "cfe-1.3", git = "https://github.com/cfe-lab/HIVIntact"} +intactness-pipeline = {ref = "cfe-1.4", git = "https://github.com/cfe-lab/HIVIntact"} [dev-packages] pytest = "*" diff --git a/Pipfile.lock b/Pipfile.lock index 840919c..05f6d7c 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "c5e8c3f18599c2490183a8f39736737ebf0b47821cc0908a613f2e95e8ee8684" + "sha256": "089fff873ef627ba4da8943f369d35baf072b48b4421d4d025abb17d951ffce8" }, "pipfile-spec": 6, "requires": { @@ -55,11 +55,11 @@ }, "certifi": { "hashes": [ - "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7", - "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716" + "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082", + "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9" ], "markers": "python_version >= '3.6'", - "version": "==2023.5.7" + "version": "==2023.7.22" }, "charset-normalizer": { "hashes": [ @@ -144,11 +144,11 @@ }, "click": { "hashes": [ - "sha256:48ee849951919527a045bfe3bf7baa8a959c423134e1a5b98c05c20ba75a1cbd", - "sha256:fa244bb30b3b5ee2cae3da8f55c9e5e0c0e86093306301fb418eb9dc40fbded5" + "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28", + "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de" ], "markers": "python_version >= '3.7'", - "version": "==8.1.6" + "version": "==8.1.7" }, "gotoh": { "git": "https://github.com/cfe-lab/MiCall.git", @@ -165,7 +165,7 @@ }, "intactness-pipeline": { "git": "https://github.com/cfe-lab/HIVIntact", - "ref": "2bb83a07b42e78a08c0f40a971d06f9393795717" + "ref": "739478485deef5fecae47e89d2baaaa16b763aef" }, "jarowinkler": { "hashes": [ @@ -342,7 +342,7 @@ "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86", "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==2.8.2" }, "python-levenshtein": { @@ -354,14 +354,16 @@ }, "pytz": { "hashes": [ - "sha256:1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588", - "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb" + "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b", + "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7" ], - "version": "==2023.3" + "version": "==2023.3.post1" }, "pyyaml": { "hashes": [ + "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5", "sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc", + "sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df", "sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741", "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206", "sha256:18aeb1bf9a78867dc38b259769503436b7c72f7a1f1f4c93ff9a17de54319b27", @@ -369,7 +371,10 @@ "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62", "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98", "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696", + "sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290", + "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9", "sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d", + "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6", "sha256:4fb147e7a67ef577a588a0e2c17b6db51dda102c71de36f8549b6816a96e1867", "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47", "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486", @@ -377,9 +382,12 @@ "sha256:596106435fa6ad000c2991a98fa58eeb8656ef2325d7e158344fb33864ed87e3", "sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007", "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938", + "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0", "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c", "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735", "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d", + "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28", + "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4", "sha256:9046c58c4395dff28dd494285c82ba00b546adfc7ef001486fbf0324bc174fba", "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8", "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5", @@ -394,7 +402,9 @@ "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43", "sha256:c8098ddcc2a85b61647b2590f825f3db38891662cfc2fc776415143f599bb859", "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673", + "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54", "sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a", + "sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b", "sha256:f003ed9ad21d6a4713f0a9b5a7a0a79e08dd0f221aff4525a2be4c346ee60aab", "sha256:f22ac1c3cac4dbc50079e965eba2c1058622631e526bd9afd45fedd49ba781fa", "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c", @@ -415,43 +425,49 @@ }, "scipy": { "hashes": [ - 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"sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32", - "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a" + "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002", + "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069" ], "index": "pypi", - "version": "==7.4.0" + "version": "==7.4.2" }, "tomli": { "hashes": [ diff --git a/Singularity b/Singularity index 66611f3..018d4df 100644 --- a/Singularity +++ b/Singularity @@ -38,7 +38,7 @@ From: ubuntu:22.04 apt-get install -y ncbi-blast+ echo ===== Installing Python packages ===== >/dev/null - pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.3 + pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.4 cd /opt/primer_finder pip3 install . diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py index d4fee4f..e088a31 100644 --- a/gene_splicer/utils.py +++ b/gene_splicer/utils.py @@ -580,7 +580,7 @@ def generate_proviral_landscape_csv(outpath, is_hivintact): table_precursor_csv = os.path.join(outpath, 'table_precursor.csv') blastn_csv = glob.glob( - os.path.join(outpath, 'hivintact*', 'blast.tsv') \ + os.path.join(outpath, 'hivintact*', 'blast.csv') \ if is_hivintact else \ os.path.join( outpath, @@ -590,25 +590,29 @@ def generate_proviral_landscape_csv(outpath, is_hivintact): ) )[0] - blastn_columns = ['qseqid', - 'qlen', - 'sseqid', - 'sgi', - 'slen', - 'qstart', - 'qend', - 'sstart', - 'send', - 'evalue', - 'bitscore', - 'length', - 'pident', - 'nident', - 'btop', - 'stitle', - 'sstrand'] with open(blastn_csv, 'r') as blastn_file: - blastn_reader = DictReader(blastn_file, fieldnames=blastn_columns, delimiter='\t') + if is_hivintact: + blastn_reader = DictReader(blastn_file) + else: + blastn_columns = ['qseqid', + 'qlen', + 'sseqid', + 'sgi', + 'slen', + 'qstart', + 'qend', + 'sstart', + 'send', + 'evalue', + 'bitscore', + 'length', + 'pident', + 'nident', + 'btop', + 'stitle', + 'sstrand'] + blastn_reader = DictReader(blastn_file, fieldnames=blastn_columns, delimiter='\t') + for row in blastn_reader: if row['qseqid'] in ['8E5LAV', 'HXB2']: # skip the positive control rows diff --git a/setup.py b/setup.py index 42a0f7d..299c967 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ 'python-Levenshtein==0.12.0', 'pandas==2.0.2', 'requests==2.31.0', - 'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.3', + 'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.4', 'pyyaml' ], package_data={