biopipen 0.7.1__py3-none-any.whl → 0.8.0__py3-none-any.whl

biopipen/scripts/vcf/VcfAnno.py

@@ -0,0 +1,26 @@
+from os import path
+import cmdy
+
+infile = {{in.infile | quote}}  # pyright: ignore
+outfile = {{out.outfile | quote}}  # pyright: ignore
+joboutdir = {{job.outdir | quote}}  # pyright: ignore
+vcfanno = {{envs.vcfanno | quote}}  # pyright: ignore
+ncores = {{envs.ncores | repr}}  # pyright: ignore
+args = {{envs.args | repr}}  # pyright: ignore
+
+{% set conf = envs.conffile or in.conffile %}
+{% if conf | isinstance: dict %}
+conffile = path.join(joboutdir, "config.toml")
+conf = {{ conf | toml | quote }}
+with open(conffile, "w") as f:
+    f.write(conf)
+{% else %}
+conffile = {{conf | quote}}
+{% endif %}
+
+args["p"] = ncores
+args["_"] = [conffile, infile]
+args["_exe"] = vcfanno
+args["_prefix"] = "-"
+
+cmdy.vcfanno(**args).r() > outfile

biopipen/scripts/vcf/VcfFix_utils.py

@@ -1,5 +1,5 @@
 import re
-
+import gzip
 from biopipen.utils.vcf import *  # noqa: F401, F403
 
 
@@ -63,7 +63,8 @@ def fix_vcffile(vcffile, outfile, fixes):
         else:
             modify_fixes.append(fix)
 
-    with open(vcffile, "r") as fin, open(outfile, "w") as fout:
+    inopen = gzip.open if vcffile.endswith(".gz") else open
+    with inopen(vcffile, "rt") as fin, open(outfile, "w") as fout:
         for line in fin:
             obj = line_to_obj(line)
             out = handle_obj(obj, modify_fixes)

{biopipen-0.7.1.dist-info → biopipen-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.7.1
+Version: 0.8.0
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -12,12 +12,11 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Provides-Extra: test
 Requires-Dist: cmdy (>=0.5,<0.6)
 Requires-Dist: datar[pandas] (>=0.11,<0.12)
-Requires-Dist: pipen (>=0.3,<0.4)
-Requires-Dist: pipen-args (>=0.3,<0.4) ; extra == "test"
-Requires-Dist: pipen-cli-run (>=0.4,<0.5)
-Requires-Dist: pipen-filters (>=0.2,<0.3)
-Requires-Dist: pipen-report (>=0.4,<0.5)
-Requires-Dist: pipen-verbose (>=0.1,<0.2) ; extra == "test"
+Requires-Dist: pipen (>=0.5,<0.6)
+Requires-Dist: pipen-args (>=0.6,<0.7)
+Requires-Dist: pipen-cli-run (>=0.5,<0.6)
+Requires-Dist: pipen-filters (>=0.4,<0.5)
+Requires-Dist: pipen-report (>=0.6,<0.7)
+Requires-Dist: pipen-verbose (>=0.3,<0.4)

{biopipen-0.7.1.dist-info → biopipen-0.8.0.dist-info}/RECORD

@@ -1,60 +1,60 @@
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+biopipen/__init__.py,sha256=kTBVFU2JV0uZaCX5p4I2Yj-xBdwAAjn3KIWXhA0k2Fw,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biopipen/core/config.py,sha256=z1b7ZHkqUzlFIvoL77NkZ8AbpUTPrP-oW-uA2Ijmi-o,1252
-biopipen/core/config.toml,sha256=I9tZTXk-TkXY-0jHdUB3XCnMWQvCqtjmHLt9MKNMkOI,1634
-biopipen/core/defaults.py,sha256=LrrvGaQ0DKrXSCnsf3dk2Jps_lUaF2_akcnwqHgfbpQ,350
-biopipen/core/filters.py,sha256=KQ4yV9Y9hdHJKiXkHxFl2h1q9V7bexxIZhgllMdJSUw,2325
-biopipen/core/proc.py,sha256=2idZID_lVZjd-va9s3rr7dnQia38r5N1T0ycFoTfOoI,521
-biopipen/core/testing.py,sha256=Su00bdQc7JNAS61i81KlnaijpvArPyzwOQJMaASfxdU,1604
+biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
+biopipen/core/config.toml,sha256=sEpvNX31ZL0XF2OpJ5tk_YJzLTwjkTf0I8-TvUfXQ3o,1598
+biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
+biopipen/core/filters.py,sha256=dJuCIrWKt7ZaHD9FPyZr65f2y9kfS2k341ayOdRefy0,2360
+biopipen/core/proc.py,sha256=enxk0Zq_UX-C62LjRk0AhS2e8B-NjvKt2rrqdTGHbe8,498
+biopipen/core/testing.py,sha256=7dC_knI-DzRtHoyEisQ73cGTNQb_kvVdMb3rDgQ4Qng,1586
 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
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-biopipen/ns/web.py,sha256=-Fr0522fOHyhCk9IsHDGp6QCWL8bQwGulrXM-ZQrujY,2371
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-biopipen/reports/cnvkit/CNVkitDiagram.svelte,sha256=pWvtmu_eZ9kqBAtIk96w68a29Q142ab461562TsiOuU,464
-biopipen/reports/cnvkit/CNVkitHeatmap.svelte,sha256=5WD4eQ7kuMyI6-yPIFIL_bqgITneKb2cG791WBDB-lw,516
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-biopipen/reports/scrna/ScFGSEA.svelte,sha256=E4G9G9nZrqesKcnpHyrFLeD7Ozsx9qwiRS3UAHkEl5I,1038
-biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=oTr1hmMAOYGEfXE80BUCUSy3M7C7f0bcrSeKDGDaRw0,4988
-biopipen/reports/scrna/SeuratPreparing.svelte,sha256=AC9O1XDTp6qvPHH4Zy4xxs5j_CEHuY3Iw-E6NPvL4iE,1198
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+biopipen/ns/vcf.py,sha256=cdkKroii0_nl_bSP2cnO09qESUAhHqu6btOiTSKS79Y,15314
+biopipen/ns/web.py,sha256=3zucrDo-IVsSnIvlw-deoScuxqWa6OMTm8Vo-R4E44Q,2224
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+biopipen/reports/cnvkit/CNVkitDiagram.svelte,sha256=SQU0ldaUtKXFYyPykxqaUofHfbuE1rNEzAUfJxZ7yz4,466
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+biopipen/reports/scrna/ScFGSEA.svelte,sha256=UXhUSGXHrzkUzFkvc9-SR5R1SlHxutgA3r7gFtvj2Xg,1040
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 biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=1AHjiInGLev1_gfis5oVegYXgKLzDXA9qMwEgPqRDfI,880
-biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubsets.svelte,sha256=ClihJi8XYvOVuipWthUfYUfHMKaAyIbQ8zh33qMrWks,990
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-biopipen/reports/tcr/Immunarch.svelte,sha256=2gjhBl3wpBP8fBEV_F1xNv_bml81f5IxeBrTXd10RQw,7871
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 biopipen/scripts/bam/CNAClinic.R,sha256=XH-J_RHMb5zh0jkaIa2UMivi13ckKZTyGWO2NxZRvQc,5000
 biopipen/scripts/bam/CNVpytor.py,sha256=5eeYgdaxOmEXRJtH1ws_CE42QmLYosXlGZln4o_aey0,12296
 biopipen/scripts/bam/ControlFREEC.py,sha256=xePG3UlIdr1hxITcF4nY_LtrBb5B9no_LUCtD6WQZWg,3142
@@ -119,7 +119,7 @@ biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=2DO
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=8hOG6FsOViXiMormMTa4tqiL9rPDUYHBnu9FdGI1tgM,7930
 biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=MGc-viCLvfmbLbW7Kc4pN13FdWXIbCkpVc1bSQwb_ek,672
 biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
-biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=klrS0LPCRM-PrGRClxQ_TEEJw3QayTpkwrrbSBeiFfk,22143
+biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
 biopipen/scripts/tcr/Attach2Seurat.R,sha256=kJck_jpjpLhUx1_9vjBeKWCrzI8Gb09nGwUOtp1Ztnk,1315
 biopipen/scripts/tcr/CloneResidency.R,sha256=Xl6kytB1ebIay0ioms1cBwWS_ayhV31U3MPY0fm2xMc,9331
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=5FPfWQjxTsv59KSDQaDWj3C95zPQMngKG7qOf95NEzI,4527
@@ -137,10 +137,11 @@ biopipen/scripts/vcf/TruvariBench.sh,sha256=80yLQ73OzSgsJ4ltzgpcWxYvvX1hFnCG8YSB
 biopipen/scripts/vcf/TruvariBenchSummary.R,sha256=YlcD9qLtK3aeW3XeLx8pXTe7yOkbaYJyLHb2TYijm8A,1474
 biopipen/scripts/vcf/TruvariConsistency.R,sha256=dqoLHCzCeyJ3JWyDX8Q8MzIFwkVK8Jg71Ml45d96Cxg,2293
 biopipen/scripts/vcf/Vcf2Bed.py,sha256=LzyJ9qW1s5mbfF8maLc77_0rE98KMc2lq1R94_NFbSU,855
+biopipen/scripts/vcf/VcfAnno.py,sha256=2Ry3lFTJN9ohDat4O6ZOtTcBLBgS6jvthx13SFhL7RY,734
 biopipen/scripts/vcf/VcfDownSample.sh,sha256=yBlyoA8xyHPkVc1XAs1biNZmN7rDR-CMz8qVh2GGvuk,939
 biopipen/scripts/vcf/VcfFilter.py,sha256=0clQi9XuN0B33xAquQ3e7ce1PZlzIOmOFctNA-dpdEw,1881
 biopipen/scripts/vcf/VcfFix.py,sha256=r2bgwwb2hAMr42wjpFZSFcUDxGllvhkOaRY_r9sKLNE,1304
-biopipen/scripts/vcf/VcfFix_utils.py,sha256=dEyc7XKYQvcIRcdwvZ4hh9q8AdsHfbl1w0Ck6v3GLAk,2220
+biopipen/scripts/vcf/VcfFix_utils.py,sha256=Ev_rvgLY9GF-aNntWbjXbl6eVlubw5uyHUD-g1c6Rno,2294
 biopipen/scripts/vcf/VcfIndex.py,sha256=1o18IY9BKb8CYUy8MXMRC4y_6yqg8BL5DTZ8VBxgy4Y,557
 biopipen/scripts/vcf/VcfIntersect.py,sha256=Bola-A_OnhpA9CKUuoJ--ijG70J55Fr9xpcNY3Ymgso,808
 biopipen/scripts/vcf/VcfLiftOver.sh,sha256=NGlLpJRcwenhbm6jmpgxK6k8VtiERNnNe7uLV6cywGc,562
@@ -156,7 +157,7 @@ biopipen/utils/plot.R,sha256=pzl37PomNeUZPxohHZ2w93j3Fc4T0Qrc62FF-9MTKdw,4417
 biopipen/utils/reference.py,sha256=-BuyiugHzy8A-JsnE7umZCJuLEJle7_oDPK0ROleoMU,3465
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.7.1.dist-info/METADATA,sha256=yk6pKE1tJGWXpHuLfkwTzUkp08UNTCuWjkY7n3AfYlo,896
-biopipen-0.7.1.dist-info/entry_points.txt,sha256=32HZbG--GdGnCHiTeBUiQ0_NkZGshITTOPE1a83-jQc,487
-biopipen-0.7.1.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-biopipen-0.7.1.dist-info/RECORD,,
+biopipen-0.8.0.dist-info/METADATA,sha256=uuLnWt_OyAoDPZvIXwKAfmw1n1OWQjAFKWjYZjpMCoA,839
+biopipen-0.8.0.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
+biopipen-0.8.0.dist-info/entry_points.txt,sha256=32HZbG--GdGnCHiTeBUiQ0_NkZGshITTOPE1a83-jQc,487
+biopipen-0.8.0.dist-info/RECORD,,

{biopipen-0.7.1.dist-info → biopipen-0.8.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.4.0
+Generator: poetry-core 1.5.1
 Root-Is-Purelib: true
 Tag: py3-none-any