Merge pull request #70 from remiolsen/dev

Merge dev

.devcontainer/devcontainer.json

@@ -0,0 +1,33 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
+{
+  "name": "Anglerfish",
+  "build": {
+    // Sets the run context to one level up instead of the .devcontainer folder.
+    "context": "..",
+    // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+    "dockerfile": "../Dockerfile",
+    // Use devcontainer target
+    "target": "devcontainer",
+  },
+  "initializeCommand": "echo 'Workaround, see github https://github.com/microsoft/vscode-remote-release/issues/9302#issuecomment-1854476541'",
+  "features": {},
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "esbenp.prettier-vscode",
+        "wholroyd.jinja",
+        "ms-python.python",
+        "[email protected]",
+        "ms-azuretools.vscode-docker",
+      ],
+    },
+  },
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  // "forwardPorts": [],
+  // "postCreateCommand": "pip3 install -e .",
+  // Configure tool-specific properties.
+  // "customizations": {},
+  // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
+  // "remoteUser": "devcontainer"
+}

.github/workflows/anglerfish.yml

@@ -19,6 +19,7 @@ jobs:
             python=${{ matrix.python-version }}
             pip
           environment-file: environment.yml
+          environment-name: anglerfish-dev
 
       # Install Anglerfish
       - shell: bash -l {0}

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 # .pre-commit-config.yaml
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.1.13
     hooks:
       - id: ruff
       - id: ruff-format

Dockerfile

@@ -1,16 +1,59 @@
-FROM mambaorg/micromamba
+FROM mambaorg/micromamba as base
 
 LABEL author="Remi-Andre Olsen" \
       description="Anglerfish development version" \
       maintainer="[email protected]"
 
 USER root
+
+# Check for arm64 architecture to install minimap2
+ARG TARGETARCH
+ENV MINIMAP_VERSION=2.26
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      # Install compliation tools for minimap2
+      apt-get update;\
+      apt-get install -y curl build-essential libz-dev;\
+      # Download minimap2
+      curl -L https://github.com/lh3/minimap2/archive/refs/tags/v${MINIMAP_VERSION}.tar.gz | tar -zxvf - ;\
+      # Compile minimap2
+      cd minimap2-${MINIMAP_VERSION};\
+      make arm_neon=1 aarch64=1; \
+      # Add to path
+      mv minimap2 /usr/local/bin/;\
+    fi
+
 COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /
-RUN micromamba env create -n anglerfish && micromamba install -y -n anglerfish -f /environment.yml && micromamba clean --all --yes 
-ENV PATH /opt/conda/envs/anglerfish/bin:$PATH
+COPY --chown=$MAMBA_USER:$MAMBA_USER requirements.txt /
+
+# Remove minimap2 from environment.yml for arm64
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      grep -v 'minimap2' /environment.yml > /environment.tmp.yml ;\
+    else \
+      cp /environment.yml /environment.tmp.yml ;\
+    fi ;\
+    chown $MAMBA_USER:$MAMBA_USER /environment.tmp.yml
 
 # Add source files to the container
 ADD . /usr/src/anglerfish
 WORKDIR /usr/src/anglerfish
-RUN eval "$(micromamba shell hook --shell bash)" && micromamba activate anglerfish && python -m pip install .[dev]
+
+# Activate the environment
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+RUN micromamba install -y -n base -f /environment.tmp.yml && micromamba clean --all --yes
+
+#####
+# Devcontainer
+#####
+FROM base as devcontainer
+
+# Useful tools for devcontainer
+RUN apt-get update;\
+    apt-get install -y git vim
+RUN eval "$(micromamba shell hook --shell bash)" && python -m pip install -e .[dev]
+
+#####
+# Main
+#####
+FROM base as main
 USER $MAMBA_USER
+RUN eval "$(micromamba shell hook --shell bash)" && python -m pip install .[dev]

README.md

@@ -33,12 +33,25 @@ conda install -c bioconda anglerfish
 pip install --upgrade --force-reinstall git+https://github.com/remiolsen/anglerfish.git
 ```
 
+### For Arm64 processors (e.g. Apple M2)
+
+Anglerfish depends on minimap2 which needs to be [compiled from source](https://github.com/lh3/minimap2?tab=readme-ov-file#installation) for Arm64 processors.
+When minimap2 is compiled and available on $PATH, anglerfish can be installed with pip:
+
+```shell
+pip install bio-anglerfish
+```
+
+Additionaly, if Docker is your cup of tea, the Dockerfile supplied in this repository should also work on both arm64 and x86 processors.
+
 ## Source development
 
 1. [Install miniconda](https://docs.conda.io/en/latest/miniconda.html).
 
 2. Set up repo clone with editable install
 
+For x86 processors (e.g. Intel/AMD):
+
 ```
 git clone https://github.com/remiolsen/anglerfish.git
 cd anglerfish
@@ -49,6 +62,18 @@ conda activate anglerfish-dev
 pip install -e ".[dev]"
 ```
 
+For Arm64 processors (e.g. Apple M1/M2). First [compile and install minimap2 manually](https://github.com/lh3/minimap2?tab=readme-ov-file#installation), then:
+
+```
+git clone https://github.com/remiolsen/anglerfish.git
+cd anglerfish
+# Create a the anglerfish conda environment (but remove minimap2)
+conda env create -f <(grep -v minimap2 environment.yml)
+# Install anglerfish
+conda activate anglerfish-dev
+pip install -e ".[dev]"
+```
+
 3. (Optional) Install pre-commit to prevent committing code that will fail linting
 
 ```
@@ -146,6 +171,16 @@ In folder `anglerfish_????_??_??_?????/`
 - `anglerfish_stats.txt` Barcode statistics from anglerfish run
 - `anglerfish_stats.json` Machine readable anglerfish statistics
 
+## Anglerfish Explore (Experimental)
+
+`anglerfish explore` is a command that aims to explore a sequencing pool without a given samplesheet and give hints on what adapter types are present, which index lenghts are used and whether there are any UMIs within the index sequence. The Anglerfish explore command is still under heavy development but can be triggered by running:
+
+```shell
+python anglerfish/explore/cli.py
+```
+
+inside the anglerfish directory.
+
 ## Credits
 
 The Anglerfish code was written by [@remiolsen](https://github.com/remiolsen) but it would not exist without the contributions of [@FranBonath](https://github.com/FranBonath), [@taborsak](https://github.com/taborsak), [@ssjunnebo](https://github.com/ssjunnebo) and Carl Rubin.

anglerfish/demux/adaptor.py

@@ -0,0 +1,69 @@
+import importlib
+import os
+
+import yaml
+
+
+class Adaptor:
+    def __init__(self, adaptors, delim, adaptor, i7_index=None, i5_index=None):
+        self.i7 = AdaptorPart(adaptors[adaptor]["i7"], adaptor, delim, i7_index)
+        self.i5 = AdaptorPart(adaptors[adaptor]["i5"], adaptor, delim, i5_index)
+        self.name = f"{adaptor}"
+        self.delim = delim
+
+    def get_i7_mask(self, insert_Ns=True):
+        return self.i7.get_mask(insert_Ns)
+
+    def get_i5_mask(self, insert_Ns=True):
+        return self.i5.get_mask(insert_Ns)
+
+    def get_fastastring(self, insert_Ns=True):
+        fasta_i5 = f">{self.name}_i5\n{self.get_i5_mask(insert_Ns)}\n"
+        fasta_i7 = f">{self.name}_i7\n{self.get_i7_mask(insert_Ns)}\n"
+        return fasta_i5 + fasta_i7
+
+
+class AdaptorPart:
+    def __init__(self, sequence, name, delim, index):
+        self.sequence = sequence
+        self.name = name
+        self.delim = delim
+        self.index = index
+
+    def has_index(self):
+        return self.sequence.find(self.delim) > -1
+
+    def len_before_index(self):
+        return self.sequence.find(self.delim)
+
+    def len_after_index(self):
+        return len(self.sequence) - self.sequence.find(self.delim) - len(self.delim)
+
+    def get_mask(self, insert_Ns):
+        if self.has_index():
+            if not insert_Ns:
+                return self.sequence.replace(self.delim, "")
+            else:
+                return self.sequence.replace(self.delim, "N" * len(self.index))
+        else:
+            return self.sequence
+
+
+# Fetch all adaptors
+def load_adaptors(raw=False):
+    p = importlib.resources.files("anglerfish.config").joinpath("adaptors.yaml")
+    assert isinstance(p, os.PathLike)
+
+    adaptors_raw = []
+    with open(p) as f:
+        adaptors_raw = yaml.safe_load(f)
+
+    if raw:
+        return adaptors_raw
+    adaptors = []
+    for adaptor in adaptors_raw:
+        adaptors.append(
+            Adaptor(adaptors_raw, "-NNN-", adaptor, i7_index=None, i5_index=None)
+        )
+
+    return adaptors

anglerfish/demux/demux.py

@@ -24,7 +24,7 @@ def parse_cs(cs_string, index, max_distance):
     return nts, lev.distance(index.lower(), nts)
 
 
-def run_minimap2(fastq_in, indexfile, output_paf, threads):
+def run_minimap2(fastq_in, indexfile, output_paf, threads, minimap_b=1):
     """
     Runs Minimap2
     """
@@ -36,24 +36,29 @@ def run_minimap2(fastq_in, indexfile, output_paf, threads):
         "10",
         "-w",
         "5",
-        "-B1",
-        "-A6",
-        "--dual=no",
+        "-A",
+        "6",
+        "-B",
+        str(minimap_b),
         "-c",
         "-t",
         str(threads),
         indexfile,
         fastq_in,
     ]
 
-    with open(output_paf, "ab") as ofile:
-        subprocess.run(cmd, stdout=ofile, check=True)
+    run_log = f"{output_paf}.log"
+    with open(output_paf, "ab") as ofile, open(run_log, "ab") as log_file:
+        p1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=log_file)
+        subprocess.run("sort", stdin=p1.stdout, stdout=ofile, check=True)
 
 
-def parse_paf_lines(paf, min_qual=10):
+def parse_paf_lines(paf, min_qual=10, complex_identifier=False):
     """
     Read and parse one paf alignment lines.
     Returns a dict with the import values for later use
+    If complex_identifier is True (default False), the keys will be on the form
+    "{read}_{i5_or_i7}_{strand_str}"
     """
     entries = {}
     with open(paf) as paf:
@@ -62,17 +67,28 @@ def parse_paf_lines(paf, min_qual=10):
             try:
                 # TODO: objectify this
                 entry = {
+                    "read": aln[0],
                     "adapter": aln[5],
                     "rlen": int(aln[1]),  # read length
                     "rstart": int(aln[2]),  # start alignment on read
                     "rend": int(aln[3]),  # end alignment on read
                     "strand": aln[4],
+                    "cg": aln[-2],  # cigar string
                     "cs": aln[-1],  # cs string
                     "q": int(aln[11]),  # Q score
                     "iseq": None,
                     "sample": None,
                 }
-                read = aln[0]
+                read = entry["read"]
+                if complex_identifier:
+                    i5_or_i7 = entry["adapter"].split("_")[-1]
+                    if entry["strand"] == "+":
+                        strand_str = "positive"
+                    else:
+                        strand_str = "negative"
+                    ix = f"{read}_{i5_or_i7}_{strand_str}"
+                else:
+                    ix = read
             except IndexError:
                 log.debug(f"Could not find all paf columns: {read}")
                 continue
@@ -81,10 +97,10 @@ def parse_paf_lines(paf, min_qual=10):
                 log.debug(f"Low quality alignment: {read}")
                 continue
 
-            if read in entries.keys():
-                entries[read].append(entry)
+            if ix in entries.keys():
+                entries[ix].append(entry)
             else:
-                entries[read] = [entry]
+                entries[ix] = [entry]
 
     return entries
 
@@ -166,14 +182,14 @@ def cluster_matches(
         fi7 = ""
         for _, adaptor, _ in sample_adaptor:
             try:
-                i5_seq = adaptor.i5_index
+                i5_seq = adaptor.i5.index
                 if i5_reversed and i5_seq is not None:
                     i5_seq = str(Seq(i5_seq).reverse_complement())
                 fi5, d1 = parse_cs(i5["cs"], i5_seq, max_distance)
             except AttributeError:
                 d1 = 0  # presumably it's single index, so no i5
 
-            i7_seq = adaptor.i7_index
+            i7_seq = adaptor.i7.index
             if i7_reversed and i7_seq is not None:
                 i7_seq = str(Seq(i7_seq).reverse_complement())
             fi7, d2 = parse_cs(i7["cs"], i7_seq, max_distance)
@@ -189,8 +205,8 @@ def cluster_matches(
             continue
         if dists[index_min] > max_distance:
             # Find only full length i7(+i5) adaptor combos. Basically a list of "known unknowns"
-            if len(fi7) + len(fi5) == len(adaptor.i7_index or "") + len(
-                adaptor.i5_index or ""
+            if len(fi7) + len(fi5) == len(adaptor.i7.index or "") + len(
+                adaptor.i5.index or ""
             ):
                 fi75 = "+".join([i for i in [fi7, fi5] if not i == ""])
                 unmatched_bed.append([read, start_insert, end_insert, fi75, "999", "."])

anglerfish/demux/report.py

@@ -97,8 +97,8 @@ def write_dataframe(self, outdir, samplesheet):
                 sen_dict = asdict(sentry)
                 if sen_dict["sample_name"] == s_dict["sample_name"]:
                     s_dict["adaptor_name"] = sen_dict["adaptor"].name
-                    s_dict["i7_index"] = sen_dict["adaptor"].i7_index
-                    s_dict["i5_index"] = sen_dict["adaptor"].i5_index
+                    s_dict["i7_index"] = sen_dict["adaptor"].i7.index
+                    s_dict["i5_index"] = sen_dict["adaptor"].i5.index
             out_list.append(s_dict)
         for key, unmatch in self.unmatched_stats.items():
             for unmatch_sample in unmatch: