biopipen 0.28.1__py3-none-any.whl → 0.29.1__py3-none-any.whl

biopipen/utils/misc.R

@@ -346,3 +346,59 @@ casename_info <- function(
     }
     out
 }
+
+run_command <- function(
+    cmd,
+    fg = FALSE,
+    wait = TRUE,
+    print_command = TRUE,
+    print_command_handler = cat,
+    ...
+) {
+    if (print_command) {
+        print_command_handler("RUNNING COMMAND:\n")
+        print_command_handler(paste0("  ", paste(cmd, collapse = " "), "\n\n"))
+    }
+
+    kwargs <- list(...)
+    stdin <- kwargs$stdin %||% ""
+    stdout <- kwargs$stdout %||% ""
+    stderr <- kwargs$stderr %||% ""
+    input <- kwargs$input %||% NULL
+    k_env <- kwargs$env %||% list()
+    env <- ""
+    if (is.list(k_env)) {
+        for (k in names(env)) { env <- paste0(env, k, "=", k_env[[k]], ";")}
+    } else {
+        env <- k_env
+    }
+    if (fg) {
+        stdout <- ""
+        stderr <- ""
+    } else {
+        if (stdout == "") { stdout <- FALSE }
+    }
+
+    command = cmd[1]
+    args = cmd[-1]
+    out <- system2(
+        command,
+        args = args,
+        stdout = stdout,
+        stderr = stderr,
+        stdin = stdin,
+        env = env,
+        wait = wait,
+        input = input
+    )
+    if (!isTRUE(stdout) && !isTRUE(stderr)) {
+        if(out != 0) stop(sprintf("Command failed with exit code %s", out))
+        if (!fg) { return(out) }
+    } else {
+        status <- attr(out, "status")
+        if (is.integer(status) && status != 0) {
+            stop(sprintf("Command failed: code (%s): %s", status, out))
+        }
+        return(out)
+    }
+}

biopipen/utils/misc.py

@@ -65,9 +65,12 @@ def run_command(
     if print_command:
         print_command_handler("RUNNING COMMAND:")
         if isinstance(cmd, str):
-            print_command_handler(f"  {cmd}")
+            print_command_handler(f"  {cmd}\n")
         else:
-            print_command_handler(f"  {shlex.join(cmd)}")
+            print_command_handler(f"  {shlex.join(cmd)}\n")
+        # flush the output if print_command_handler is print
+        if print_command_handler is print:
+            sys.stdout.flush()
 
     if isinstance(cmd, str):
         kwargs["shell"] = True

biopipen/utils/reference.py

@@ -1,5 +1,10 @@
+"""Utilities for indexing reference files"""
+from __future__ import annotations
+
 import tempfile
+from os import PathLike
 from pathlib import Path
+from typing import Literal
 
 from ..core.config import config
 from biopipen.utils.misc import run_command
@@ -18,7 +23,12 @@ def gztype(gzfile):
     return "flat"
 
 
-def tabix_index(infile, preset, tmpdir=None, tabix=config.exe.tabix):
+def tabix_index(
+    infile: str | PathLike,
+    preset: Literal["gff", "bed", "sam", "vcf", "gaf"],
+    tmpdir: bool | str | PathLike | None = None,
+    tabix: str = config.exe.tabix,
+) -> str | PathLike:
     """Index input file using tabix
 
     1. Try to check if there is an index file in the same directory where infile
@@ -28,22 +38,47 @@ def tabix_index(infile, preset, tmpdir=None, tabix=config.exe.tabix):
        it in tmpdir
     4. Index the bgzipped file and return the bgzipped file
 
+    Args:
+        infile: The input file to be indexed
+        preset: The preset used to index the file
+        tmpdir: The directory to link the infile there and index it
+            If False, try to index the infile directly. The directory where
+            the infile is should be writable.
+        tabix: The path to tabix
+
     Returns:
         The infile itself or re-bgzipped infile. This file comes with the
         index file in the same directory
     """
-    if tmpdir is None:
-        tmpdir = Path(tempfile.mkdtemp(prefix="biopipen_tabix_index_"))
-    else:
-        tmpdir = Path(tmpdir)
 
     infile = Path(infile)
     gt = gztype(infile)
-
-    if gt == "bgzip" and infile.with_suffix(infile.suffix + ".tbi").is_file():
+    index_file = infile.with_suffix(infile.suffix + ".tbi")
+    # if index file exists, and it's newer than the infile, return infile
+    if (
+        gt == "bgzip"
+        and index_file.is_file()
+        and index_file.stat().st_mtime > infile.resolve().stat().st_mtime
+    ):
         # only bgzipped file is possible to have index file
         return infile
 
+    if tmpdir is False:
+        # index the infile directly
+        run_command([tabix, "-p", preset, infile], fg=True)
+        return infile
+
+    if tmpdir is None:
+        from hashlib import md5
+        # use a hash of infile to create the tempdir
+        tmpdir = Path(tempfile.gettempdir()).joinpath(
+            f"biopipen_tabix_index_{md5(str(infile).encode()).hexdigest()}"
+        )
+    else:
+        tmpdir = Path(tmpdir)
+
+    tmpdir.mkdir(exist_ok=True, parents=True)
+
     # /path/to/some.vcf -> some.vcf
     # /path/to/some.vcf.gz -> some.vcf
     basename = infile.stem if infile.name.endswith(".gz") else infile.name
@@ -53,15 +88,24 @@ def tabix_index(infile, preset, tmpdir=None, tabix=config.exe.tabix):
     if gt == "gzip":
         # re-bgzip
         run_command(
-            ["gunzip", "-c", infile], stdout=new_infile.with_suffix(""),
+            ["gunzip", "-f", "-c", infile], stdout=new_infile.with_suffix(""),
         )
-        run_command(["bgzip", new_infile.with_suffix("")], fg=True)
+        run_command(["bgzip", "-f", new_infile.with_suffix("")], fg=True)
     elif gt == "flat":
-        run_command(["bgzip", "-c", infile], stdout=new_infile)
+        run_command(["bgzip", "-f", "-c", infile], stdout=new_infile)
     else:
+        if new_infile.is_symlink():
+            new_infile.unlink()
         # directory of infile may not have write permission
         new_infile.symlink_to(infile)
 
+    new_index_file = new_infile.with_suffix(new_infile.suffix + ".tbi")
+    if (
+        new_index_file.is_file()
+        and new_index_file.stat().st_mtime > infile.resolve().stat().st_mtime
+    ):
+        return new_infile
+
     run_command([tabix, "-p", preset, new_infile], fg=True)
     return new_infile
 

{biopipen-0.28.1.dist-info → biopipen-0.29.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.28.1
+Version: 0.29.1
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -16,7 +16,7 @@ Provides-Extra: runinfo
 Requires-Dist: datar[pandas] (>=0.15.6,<0.16.0)
 Requires-Dist: pipen-board[report] (>=0.15,<0.16)
 Requires-Dist: pipen-cli-run (>=0.13,<0.14)
-Requires-Dist: pipen-filters (>=0.12,<0.13)
+Requires-Dist: pipen-filters (>=0.13,<0.14)
 Requires-Dist: pipen-poplog (>=0.1.2,<0.2.0)
 Requires-Dist: pipen-runinfo (>=0.6,<0.7) ; extra == "runinfo"
 Requires-Dist: pipen-verbose (>=0.11,<0.12)

{biopipen-0.28.1.dist-info → biopipen-0.29.1.dist-info}/RECORD

@@ -1,33 +1,33 @@
-biopipen/__init__.py,sha256=ZRQKbgDaGz_yuLk-cUKuk6ZBKCSRKZC8nQd041NRNXk,23
+biopipen/__init__.py,sha256=QTaZs8dGSlxK5ryfzkJ2KhyNkszMPGsEYfsjGAbckck,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
-biopipen/core/config.toml,sha256=20RCI30Peee1EQdfb_UbV3Hf74XUPndJnYZlUThytsw,1781
+biopipen/core/config.toml,sha256=IL31RfhuF-6V46lvLs1F-Z4SPmUuTvWzk5PN37Xjrqc,1907
 biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
 biopipen/core/filters.py,sha256=-OIzS5F_yNZ0Nk5Ci16BepPWqLOGBmYVqX3W98RSK9Y,12488
 biopipen/core/proc.py,sha256=60lUP3PcUAaKbDETo9N5PEIoeOYrLgcSmuytmrhcx8g,912
 biopipen/core/testing.py,sha256=lZ_R5ZbYPO2NPuLHdbzg6HbD_f4j8paVVbyeUqwg6FE,3411
 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biopipen/ns/bam.py,sha256=5AsYrB0mtr_mH6mCL6gjJ5rC4NywpjFkpFjUrBGp7Fk,9301
-biopipen/ns/bcftools.py,sha256=puCDfIL-1z6cz2y1Rlz-ESNIr8xJgeIjEQ440qicCvM,3467
-biopipen/ns/bed.py,sha256=UN38qUChDeE-ipuSBY8RVLwvJqM2wxSRmlhOiDo4JG0,5395
+biopipen/ns/bam.py,sha256=jLhIztPiKsGfMpDgbcEpsybFskKkquIx9OKyTOc_L7Q,9172
+biopipen/ns/bed.py,sha256=HsTCJge7XNfCZyCBJ4iifNKQ5we4VZSpRx8XL8--y5A,6689
 biopipen/ns/cellranger.py,sha256=yPBoNzVSY74J7uyVucaob5lqZKKru5-hYSM4f4Nr2OY,5553
-biopipen/ns/cellranger_pipeline.py,sha256=lyRUdJEeQaTWGUz5UbrSdHMH_cgzXAXLlERmanppEBs,4037
-biopipen/ns/cnv.py,sha256=vq6dZfEOyuVuqg3nP6FQtNmQ-JocpBJMX9IYlZ0OPD0,6803
+biopipen/ns/cellranger_pipeline.py,sha256=EWkPJTujamNSMQoRnKfhUiIj6TkMfRmCSUbPfd8Tv8E,4011
+biopipen/ns/cnv.py,sha256=ssQAHf2MB675avoXVRkYy0vGiqIpRpRExywjhbymmBI,7811
 biopipen/ns/cnvkit.py,sha256=5mA2Q8-YDs4g1HoxtpB_NWnyZYwEThNr3s3wlubLQrQ,31130
-biopipen/ns/cnvkit_pipeline.py,sha256=2fJLn70L2jJ81ZMNdnU84Sf3HoKA2CSnHuDzLGR8jmw,36854
+biopipen/ns/cnvkit_pipeline.py,sha256=DZZljwvwVEI9sRUYBdxkOIT5-CIPLH1tag_OIU86aes,37094
 biopipen/ns/delim.py,sha256=fejsh4KW1TG5oMZzAC238LvQhBz7brXkfl3BHfnLK5M,5612
-biopipen/ns/gene.py,sha256=Q5FzRByfnRITXRNRZR65ApG09FRyiihRC3TcIXxufzE,2228
+biopipen/ns/gene.py,sha256=rty-Bjcf87v2vyb9X4kRvfrQ6XQYXgN4f2ftFO0nWA8,3888
 biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
-biopipen/ns/misc.py,sha256=fzn0pXvdghMkQhu-e3MMapPNMyO6IAJbtTzVU3GbFa0,3246
-biopipen/ns/plot.py,sha256=fzJAKKl4a_tsVkLREGCQTFVHP049m33LdWgeYRb6v7M,5483
+biopipen/ns/misc.py,sha256=qXcm0RdR6W-xpYGgQn3v7JBeYRWwVm5gtgSj2tdVxx4,2935
+biopipen/ns/plot.py,sha256=r0n10N9iipZgbDZzkJVq4-9drMtinGK0ntBa3Lk2JFc,15771
+biopipen/ns/regulatory.py,sha256=qvc9QrwgwCI_lg0DQ2QOZbAhC8BAD1qnQXSGtAGlVcY,11750
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=OCEuE-TcqR7ADEEsgA6qL9rDK5R75YWRmmmvaNIFtZU,105925
+biopipen/ns/scrna.py,sha256=0MG0uyyrlSfjS-Lp2Abm_4f4LnLwyjUd6mIOtaQv36Q,108085
 biopipen/ns/scrna_metabolic_landscape.py,sha256=6AhaynGG3lNRi96N2tReVT46BJMuEwooSSd2irBoN80,28347
-biopipen/ns/snp.py,sha256=EQ2FS0trQ7YThPmBVTpS66lc2OSfgQ6lCh6WnyP-C2g,5499
-biopipen/ns/stats.py,sha256=yJ6C1CXF84T7DDs9mgufqUOr89Rl6kybE5ji8Vnx6cw,13693
+biopipen/ns/snp.py,sha256=-Jx5Hsv_7KV7TqLU0nHCaPkMEN0CFdi4tNVlyq0rUZ4,27259
+biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
 biopipen/ns/tcr.py,sha256=0PCF8iPZ629z6P3RHoAWEpMWmuDslomTGcMopjqvXmE,88304
-biopipen/ns/vcf.py,sha256=cdkKroii0_nl_bSP2cnO09qESUAhHqu6btOiTSKS79Y,15314
+biopipen/ns/vcf.py,sha256=0aKH_YSLy_-JzV-_VZb0EoScv7JKGrDU7BaeWHjDuRo,22699
 biopipen/ns/web.py,sha256=3zucrDo-IVsSnIvlw-deoScuxqWa6OMTm8Vo-R4E44Q,2224
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
 biopipen/reports/bam/CNVpytor.svelte,sha256=s03SlhbEPd8-_44Dy_cqE8FSErhUdqStLK39te5o7ZE,1364
@@ -58,6 +58,11 @@ biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=4M8V6
 biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte,sha256=7FohWYR2BEqo77W4FuGsuwEEvG7j_Mc2ohXG8TSgODg,907
 biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=bbPWDEXTi-A377Vo2VaEyh_VoxGmFj-P3WX8g_y_-9k,3416
 biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=TohFc1IsHFAio8WNu_1FoaJucxsW3OtmS7fIJOH5KHc,350
+biopipen/reports/snp/PlinkCallRate.svelte,sha256=QoHqzJ88sx8d8FfH4ToFcR690RX0jmi2SaeWVAnw8y0,730
+biopipen/reports/snp/PlinkFreq.svelte,sha256=gHN1SezJ5l732Ndtrl_xZABdWPoSvAWkRh1rKbcsD1c,535
+biopipen/reports/snp/PlinkHWE.svelte,sha256=nes-NTwatoxvLoRBCg6jPp0fSg5kZZkVngURpfmM_nc,502
+biopipen/reports/snp/PlinkHet.svelte,sha256=hlSGx3qVETvZg6cd6vf27EtGeRzwD86I01kMLyIHEC4,545
+biopipen/reports/snp/PlinkIBD.svelte,sha256=s7nepF52Q4hKhRnIZDTFXqG7SIvhGy0NtfnTpexG0mE,507
 biopipen/reports/tcr/CDR3AAPhyschem.svelte,sha256=_r1pi_yTu_KjC02aegZ52IEQY8Mq0p3nqW_o9wOFWf8,1530
 biopipen/reports/tcr/CloneResidency.svelte,sha256=pzjkdGAhB7STxlXkTY5wnTT3plhkAPKMdGa6jwKuwoc,470
 biopipen/reports/tcr/Immunarch.svelte,sha256=jHOGUCWREaDNUf1_s6h9Kx_sp-y_dDRqY1rWrx0o0LM,433
@@ -72,47 +77,55 @@ biopipen/reports/vcf/TruvariConsistency.svelte,sha256=BBvtxi1EPmGH7j5M5zMOcLEhKW
 biopipen/scripts/bam/BamMerge.py,sha256=jyaJI0-TulAxaCzvrYjC8PujH_ECNInevnPbh2_XQtU,3477
 biopipen/scripts/bam/BamSplitChroms.py,sha256=b7GS2I4X0dLOhlPg_r9-buoIHTWlq6zHI3Rox94LXR8,4893
 biopipen/scripts/bam/CNAClinic.R,sha256=EbQ1s1_y2uCERTP1aP0Fwu_dO4n8k1YSMBswwVs0uDQ,5040
-biopipen/scripts/bam/CNVpytor.py,sha256=k7Ue_jh5Rp-qi6VDjkqLvbA47rMAyI-NBx7lv_otd2I,12893
+biopipen/scripts/bam/CNVpytor.py,sha256=hOUli9BDMOoth0or-tjUYC1AP3yNOuxUS6G3Rhcg99s,18000
 biopipen/scripts/bam/ControlFREEC.py,sha256=oX6iWsos-CfiT_ViDBrKeMOOIVdCKWrB-_MqzLgEF9s,3267
-biopipen/scripts/bcftools/BcftoolsAnnotate.py,sha256=0OIiP9bfR81vU1fbVgRPh8j860AEUPJ4yWFQvuZNiuI,1339
-biopipen/scripts/bcftools/BcftoolsFilter.py,sha256=P7OV9fwMSfFgD7ZtLWrU1-T2Oph94ACqtBMGi-SYrOk,2278
-biopipen/scripts/bcftools/BcftoolsSort.py,sha256=0xXIUf1Po8QHe8XTC5SyU_6kmLopRgp8Z87NXwWl8Mc,639
 biopipen/scripts/bed/Bed2Vcf.py,sha256=u0mp_2Y4UtEA839zq9UENesH6Gyiwd4sZQW9wFnBVU0,5090
 biopipen/scripts/bed/BedConsensus.py,sha256=gfAxuIalvCEpS0tiOyAJGPYGgHN0L-hm0K37Iteh5yw,2386
 biopipen/scripts/bed/BedLiftOver.sh,sha256=Y4gBsz9w4zhE29UmWojO6F4PXMMMWC1uCzjrxa19eOs,256
-biopipen/scripts/bed/BedtoolsMerge.py,sha256=TjKO5MpUzDj931bQAWku2660MVSiZzdMHt_v2Xbt0IE,355
+biopipen/scripts/bed/BedtoolsIntersect.py,sha256=sFyXPL3kG59xa5eJwHumcQLw3lfabOXsq2-k8IgIqt4,1722
+biopipen/scripts/bed/BedtoolsMerge.py,sha256=7mt307V_wWa_ME0VfuMsVX0HgEwfDcZtY_bDvOPjFiQ,368
 biopipen/scripts/cellranger/CellRangerCount.py,sha256=Mi6PiufFPp-cb4WRgZhniXi2ja5VUusRDW9RdAqFyX0,2831
 biopipen/scripts/cellranger/CellRangerSummary.R,sha256=8EqP4j074RLi5Adw47xyqQwkDEcvSS6Yfk0UgKKYOuo,11045
 biopipen/scripts/cellranger/CellRangerVdj.py,sha256=ipGkPzkiVy5IpPrYKUK4zgEIvz-aMJOKbMEN-bMStFE,2200
-biopipen/scripts/cnv/AneuploidyScore.R,sha256=liAN8u8_lj8voJ01oBW9Dw09yi388KF5f_gwPOv0wdE,8437
-biopipen/scripts/cnv/AneuploidyScoreSummary.R,sha256=9Zni5zqYfzevs5XSAt3fqD9WZ_RWr_ByUnXReKLLWoY,12337
-biopipen/scripts/cnv/TMADScore.R,sha256=uCLHQR6sMt-4uVUAEJlJxYXlai9ZE5J7xBl0sl-EkjU,1065
-biopipen/scripts/cnv/TMADScoreSummary.R,sha256=xcuEzHpzPNWWdZlurp5PS4D7665ZvIJtc4739pFACPI,7003
-biopipen/scripts/cnvkit/CNVkitAccess.py,sha256=l94f9L_C-tcNCFGCzZ7YQEZTBdpteY5Fq5DPAYu3zAI,645
-biopipen/scripts/cnvkit/CNVkitAutobin.py,sha256=Fy2f4IjNMaFyikdjSXEkkuf-bSwLggfwWpe4SOvZvPk,1593
-biopipen/scripts/cnvkit/CNVkitBatch.py,sha256=QhXwTkdJcP6woyuJgctJWaNURxJcb_xwID05lEapCcc,3775
+biopipen/scripts/cnv/AneuploidyScore.R,sha256=OldqRUr4rn8AZZCLDaX5xCIR1e0R7XXb_RQ2hXDHHog,9142
+biopipen/scripts/cnv/AneuploidyScoreSummary.R,sha256=fhffzQ5tW13KSgGz9CNDmvgqxUR1NDVVrsW_5xl1968,12410
+biopipen/scripts/cnv/TMADScore.R,sha256=IH07REfBO3QB2QNWuwGY6LgAUAOE0lsfP6W0bS67zGs,1530
+biopipen/scripts/cnv/TMADScoreSummary.R,sha256=w58LD5xHnLal9jv53nBUGpQ8eTkAyEk1leCVN2T_ZaM,7109
+biopipen/scripts/cnvkit/CNVkitAccess.py,sha256=UerX66utY8UdlI1mlSVD7E9O0ByLnHzt6G3Urb8mCWE,689
+biopipen/scripts/cnvkit/CNVkitAutobin.py,sha256=H5YcQ8f7Vs01Wad_oEQ9_AKBo5bKW856hAxShD75oDA,1656
+biopipen/scripts/cnvkit/CNVkitBatch.py,sha256=uzb300XLPRzV1BOOug6dAmupZ5FtQamFoYslVmbdTCA,3794
 biopipen/scripts/cnvkit/CNVkitCall.py,sha256=NyOnMjwT4w-ID9YtNks6fp6BIG7OzkGHmYphcXzAy_M,3544
-biopipen/scripts/cnvkit/CNVkitCoverage.py,sha256=t-PjHi0WujpAyhV_KgYIk4j6J-taY4ikdXJwdY96KSc,779
+biopipen/scripts/cnvkit/CNVkitCoverage.py,sha256=hTXh77QmMWy12Ipphdabkai19D0ZfKd7XF5Soc-HSG8,823
 biopipen/scripts/cnvkit/CNVkitDiagram.py,sha256=tvHW6wAZ9YXKb6sbdvWEO_HPjLK4LOYxrcnPkV8iUoA,1889
 biopipen/scripts/cnvkit/CNVkitFix.py,sha256=nZ7_15ba4zgTRpyQfyGAdcx1kCWyNTyjfEkKYxQumJA,1087
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@@ -130,7 +143,7 @@ biopipen/scripts/scrna/ExprImputation-alra.R,sha256=w3W1txJcdWg52-SETY2Z0lO7maDN
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@@ -143,14 +156,14 @@ biopipen/scripts/scrna/SeuratClusterStats-hists.R,sha256=YhuD-GePjJPSkR0iLRgV_hi
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@@ -161,12 +174,23 @@ biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=sOnHSH0Ld-
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@@ -193,7 +217,7 @@ biopipen/scripts/tcr/ImmunarchFilter.R,sha256=o25O36FwH_0w6F8DFQ0SfpcwDzlzaGefXq
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@@ -210,6 +234,10 @@ biopipen/scripts/tcr/TESSA_source/utility.R,sha256=6qbkMV7yp4bgQe718QiASQUAgOE2e
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@@ -218,29 +246,30 @@ biopipen/scripts/vcf/VcfAnno.py,sha256=FW626rAs_WSU7AHQMKjfkYoByUGh_gVyJM97neGfO
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 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.28.1.dist-info/METADATA,sha256=UPLio_HdqVCyeNe2VCcUTZXz1CGakrQFH7_Dbb9qnHQ,882
-biopipen-0.28.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.28.1.dist-info/entry_points.txt,sha256=wu70aoBcv1UahVbB_5237MY-9M9_mzqmWjDD-oi3yz0,621
-biopipen-0.28.1.dist-info/RECORD,,
+biopipen-0.29.1.dist-info/METADATA,sha256=62K0OT3uiUi6Gnt0WGHGaox3WNV7hsbUsg60iPCc4nU,882
+biopipen-0.29.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.29.1.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
+biopipen-0.29.1.dist-info/RECORD,,

{biopipen-0.28.1.dist-info → biopipen-0.29.1.dist-info}/entry_points.txt

@@ -1,6 +1,5 @@
 [pipen_cli_run]
 bam=biopipen.ns.bam
-bcftools=biopipen.ns.bcftools
 bed=biopipen.ns.bed
 cellranger=biopipen.ns.cellranger
 cellranger_pipeline=biopipen.ns.cellranger_pipeline
@@ -12,6 +11,7 @@ gene=biopipen.ns.gene
 gsea=biopipen.ns.gsea
 misc=biopipen.ns.misc
 plot=biopipen.ns.plot
+regulatory=biopipen.ns.regulatory
 rnaseq=biopipen.ns.rnaseq
 scrna=biopipen.ns.scrna
 scrna_metabolic_landscape=biopipen.ns.scrna_metabolic_landscape

biopipen/ns/bcftools.py

@@ -1,111 +0,0 @@
-"""handling VCF files using bcftools"""
-from ..core.proc import Proc
-from ..core.config import config
-
-
-class BcftoolsAnnotate(Proc):
-    """Add or remove annotations from VCF files
-
-    Input:
-        infile: The input VCF file
-        annfile: The annotation file
-
-    Output:
-        outfile: The annotated VCF file
-
-    Envs:
-        bcftools: Path to bcftools
-        tabix: Path to tabix, used to index infile and annfile
-        annfile: The annotation file. If `in.annfile` is provided,
-            this is ignored
-        ncores: Number of cores (`--nthread`) to use
-        cols: Overwrite `-c/--columns`
-        header: Headers to be added
-        args: Other arguments for `bcftools annotate`
-    """
-    input = "infile:file, annfile:file"
-    output = "outfile:file:{{in.infile | basename}}"
-    lang = config.lang.python
-    envs = {
-        "bcftools": config.exe.bcftools,
-        "tabix": config.exe.tabix,
-        "annfile": "",
-        "cols": [],
-        "header": [],
-        "args": {},
-        "ncores": config.misc.ncores,
-    }
-    script = "file://../scripts/bcftools/BcftoolsAnnotate.py"
-
-
-class BcftoolsFilter(Proc):
-    """Apply fixed threshold filters to VCF files
-
-    Input:
-        infile: The input VCF file
-
-    Output:
-        outfile: The filtered VCF file. If the `in.infile` is gzipped, this is
-            gzipped as well.
-
-    Envs:
-        bcftools: Path to bcftools
-        ncores: Number of cores (`--nthread`) to use
-        keep: Whether we should keep the filtered variants or not.
-        args: Other arguments for `bcftools annotate`
-        ncores: `nthread`
-        tmpdir: Path to save the intermediate files
-            Since the filters need to be applied one by one by bcftools
-        includes: and
-        excludes: include/exclude only sites for which EXPRESSION is true.
-            See: https://samtools.github.io/bcftools/bcftools.html#expressions
-            If provided, `envs.args.include/exclude` will be ignored.
-            If `str`/`list` used, The filter names will be `Filter%d`
-            A dict is used when keys are filter names and values are expressions
-    """
-    input = "infile:file"
-    output = "outfile:file:{{in.infile | basename}}"
-    lang = config.lang.python
-    envs = {
-        "bcftools": config.exe.bcftools,
-        "keep": True,
-        "ncores": config.misc.ncores,
-        "includes": None,
-        "excludes": None,
-        "tmpdir": config.path.tmpdir,
-        "args": {},
-    }
-    script = "file://../scripts/bcftools/BcftoolsFilter.py"
-
-
-class BcftoolsSort(Proc):
-    """Sort VCF files
-
-    Input:
-        infile: The input VCF file
-
-    Output:
-        outfile: The sorted VCF file.
-
-    Envs:
-        bcftools: Path to bcftools
-        gz: Whether to gzip the output file
-        index: Whether to index the output file (tbi) (`envs.gz` forced to True)
-        tmpdir: Path to save the intermediate files
-        args: Other arguments for `bcftools sort`. For example `max-mem`.
-            See also https://samtools.github.io/bcftools/bcftools.html#sort
-    """
-    input = "infile:file"
-    output = (
-        "outfile:file:{{in.infile | stem0}}.vcf"
-        "{% if envs.gz or envs.index %}.gz{% endif %}"
-    )
-    lang = config.lang.python
-    envs = {
-        "bcftools": config.exe.bcftools,
-        "gz": True,
-        "index": True,
-        "tmpdir": config.path.tmpdir,
-        "args": {},
-    }
-    script = "file://../scripts/bcftools/BcftoolsSort.py"

biopipen/scripts/bcftools/BcftoolsAnnotate.py

@@ -1,42 +0,0 @@
-from os import path
-
-from biopipen.utils.reference import tabix_index
-from biopipen.utils.misc import dict_to_cli_args, run_command
-
-infile = {{in.infile | repr}}  # pyright: ignore
-annfile = {{(in.annfile or envs.annfile) | repr}}  # pyright: ignore
-outfile = {{out.outfile | repr}}  # pyright: ignore
-joboutdir = {{job.outdir | repr}}  # pyright: ignore
-bcftools = {{envs.bcftools | repr}}  # pyright: ignore
-tabix = {{envs.tabix | repr}}  # pyright: ignore
-ncores = {{envs.ncores | repr}}  # pyright: ignore
-cols = {{envs.cols | repr}}  # pyright: ignore
-header = {{envs.header | repr}}  # pyright: ignore
-args = {{envs.args | repr}}  # pyright: ignore
-
-args[""] = bcftools
-args["_"] = tabix_index(infile, "vcf")
-args["o"] = outfile
-args["threads"] = ncores
-
-if annfile:
-    abname = path.basename(annfile)
-    ext = path.splitext(
-        abname[:-3] if abname.endswith('.gz') else abname
-    )[-1][1:]
-    args["a"] = tabix_index(annfile, ext, tabix)
-
-if cols and isinstance(cols, list):
-    args["c"] = ",".join(cols)
-
-if header:
-    if not isinstance(header, list):
-        header = [header]
-
-    headerfile = path.join(joboutdir, "header.txt")
-    with open(headerfile, "w") as fh:
-        for head in header:
-            fh.write(f"{head}\n")
-    args["h"] = headerfile
-
-run_command(dict_to_cli_args(args, dashify=True), fg=True)