Merge pull request #13 from Psy-Fer/dev

v0.1.1 to add pore_type
Psy-Fer · Jul 4, 2024 · e83526d · e83526d
2 parents 2af0d24 + 0f41eed
commit e83526d
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diff --git a/.github/workflows/snake.yml b/.github/workflows/snake.yml
@@ -16,8 +16,8 @@ jobs:
         submodules: recursive
     - name: install packages
       run: sudo apt-get update && sudo apt-get install -y zlib1g-dev gcc python3 python3-pip && pip3 install setuptools cython numpy
-    - name: slow5lib-dev
-      run: git clone -b dev https://github.com/hasindu2008/slow5lib && cd slow5lib && python3 setup.py install --user && cd ..
+    - name: slow5lib
+      run: git clone https://github.com/hasindu2008/slow5lib && cd slow5lib && python3 setup.py install --user && cd ..
     - name: install
       run:  python3 setup.py install --user && blue-crab --help
     - name: test
@@ -31,8 +31,8 @@ jobs:
         submodules: recursive
     - name: install packages
       run: sudo apt-get update && sudo apt-get install -y zlib1g-dev gcc python3 python3-pip && pip3 install setuptools cython numpy
-    - name: slow5lib-dev
-      run: git clone -b dev https://github.com/hasindu2008/slow5lib && cd slow5lib && python3 setup.py install --user && cd ..
+    - name: slow5lib
+      run: git clone https://github.com/hasindu2008/slow5lib && cd slow5lib && python3 setup.py install --user && cd ..
     - name: install
       run:  python3 setup.py install --user && blue-crab --help
     - name: test
@@ -46,45 +46,30 @@ jobs:
         submodules: recursive
     - name: install packages
       run: sudo apt-get update && sudo apt-get install -y zlib1g-dev gcc python3 python3-pip && pip3 install --break-system-packages setuptools cython numpy
-    - name: slow5lib-dev
-      run: git clone -b dev https://github.com/hasindu2008/slow5lib && cd slow5lib && python3 setup.py install --user && cd ..
+    - name: slow5lib
+      run: git clone https://github.com/hasindu2008/slow5lib && cd slow5lib && python3 setup.py install --user && cd ..
     - name: install
       run:  python3 setup.py install --user && blue-crab --help
     - name: test
-      run: test/test.sh      
-  # arm64:
-  #   name: pyslow5 ubuntu arm
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #   - run: docker run --rm --privileged multiarch/qemu-user-static:register --reset
-  #   - uses: docker://multiarch/ubuntu-core:arm64-focal
-  #     with:
-  #       args: 'uname -a'
-  #   - uses: actions/checkout@v1
-  #   - uses: docker://multiarch/ubuntu-core:arm64-focal
-  #     with:
-  #       args: >
-  #         bash -c "apt-get update &&
-  #         apt-get install -y zlib1g-dev gcc make python3 python3-pip git wget &&
-  #         pip3 install setuptools cython numpy &&
-  #         ldd --version && gcc --version && python3 --version &&
-  #         git clone -b dev https://github.com/hasindu2008/slow5lib && cd slow5lib && python3 setup.py install && cd .. &&
-  #         python3 setup.py install && blue-crab --help && test/test.sh"
-  # os_x_11:
-  #   name: macos-11
-  #   runs-on: macos-11
-  #   steps:
-  #   - uses: actions/checkout@v2
-  #     with:
-  #       submodules: recursive
-  #   - name: install packages
-  #     run: pip3 install numpy
-  #   - name: slow5lib-dev
-  #     run: git clone https://github.com/hasindu2008/slow5lib && cd slow5lib && pip3 install . && cd ..
-  #   - name: install
-  #     run:  pip3 install . && blue-crab --help
-  #   - name: test
-  #     run: test/test.sh
+      run: test/test.sh
+  arm64:
+    name: pyslow5 ubuntu arm
+    runs-on: ubuntu-latest
+    steps:
+    - run: docker run --rm --privileged multiarch/qemu-user-static:register --reset
+    - uses: docker://multiarch/ubuntu-core:arm64-focal
+      with:
+        args: 'uname -a'
+    - uses: actions/checkout@v1
+    - uses: docker://multiarch/ubuntu-core:arm64-focal
+      with:
+        args: >
+          bash -c "apt-get update &&
+          apt-get install -y zlib1g-dev gcc make python3 python3-pip git wget &&
+          pip3 install setuptools cython numpy &&
+          ldd --version && gcc --version && python3 --version &&
+          git clone https://github.com/hasindu2008/slow5lib && cd slow5lib && pip3 install . && cd .. &&
+          pip3 install --upgrade pip && rm /usr/lib/python3/dist-packages/pip && pip3 --version && pip3 install .  && blue-crab --help && test/test.sh"
   os_x_12:
     name: macos-12
     runs-on: macos-12
@@ -94,7 +79,7 @@ jobs:
         submodules: recursive
     - name: install packages
       run: pip3 install numpy
-    - name: slow5lib-dev
+    - name: slow5lib
       run: git clone https://github.com/hasindu2008/slow5lib && cd slow5lib  && pip3 install . && cd ..
     - name: install
       run:  pip3 install . && blue-crab --help
@@ -109,12 +94,12 @@ jobs:
         submodules: recursive
     - name: install packages
       run: pip3 install numpy
-    - name: slow5lib-dev
+    - name: slow5lib
       run: git clone https://github.com/hasindu2008/slow5lib && cd slow5lib  && pip3 install . && cd ..
     - name: install
       run:  pip3 install . && blue-crab --help
     - name: test
-      run: test/test.sh      
+      run: test/test.sh
   os_x_14:
     name: macos-14
     runs-on: macos-14
@@ -124,9 +109,9 @@ jobs:
         submodules: recursive
     - name: install packages
       run: pip3 install --break-system-packages numpy
-    - name: slow5lib-dev
+    - name: slow5lib
       run: git clone https://github.com/hasindu2008/slow5lib && cd slow5lib  && pip3 install --break-system-packages . && cd ..
     - name: install
       run:  pip3 install --break-system-packages . && blue-crab --help
     - name: test
-      run: test/test.sh      
+      run: test/test.sh
diff --git a/src/_version.py b/src/_version.py
@@ -1 +1 @@
-__version__="0.1.0"
+__version__="0.1.1"
diff --git a/src/blue_crab.py b/src/blue_crab.py
@@ -137,7 +137,7 @@ def get_data_from_pod5_record(read):
     predicted_scaling = read.predicted_scaling
     predicted_scaling_shift = predicted_scaling.shift
     predicted_scaling_scale = predicted_scaling.scale
-    if pore_data.pore_type not in ["not_set", ""]:
+    if pore_data.pore_type not in ["not_set", "R10.4.1", ""]:
         logger.error("pore_type is '{}' expected to be 'not_set'. Please contact developers with this message.".format(pore_data.pore_type))
         kill_program()
 
@@ -753,6 +753,11 @@ def m2m_s2p_worker(args, input_queue, pod5_out):
                 slow5_end_reason_labels = s5.get_aux_enum_labels("end_reason")
             except:
                 slow5_end_reason_labels = ['unknown']
+
+            # if the above fails, it goes to unknown, but if it doesn't exist, it returns and empty list
+            # so let's set it to unknown
+            if len(slow5_end_reason_labels) < 1:
+                slow5_end_reason_labels = ['unknown']
             # before ONT added DATA_SERVICE_UNBLOCK_MUX_CHANGE in the middle and removed partial...
             # slow5_end_reason_labels = ['unknown', 'partial', 'mux_change', 'unblock_mux_change', 'signal_positive', 'signal_negative']
             for read in reads:
@@ -774,7 +779,12 @@ def m2m_s2p_worker(args, input_queue, pod5_out):
                 # sampling_frequency = read["sampling_rate"]
                 # map end_reason if present
                 # let's convert this to it's string equivalent
-                s5_end_reason = slow5_end_reason_labels[read.get("end_reason", 0)]
+                try:
+                    s5_end_reason = slow5_end_reason_labels[read.get("end_reason", 0)]
+                except Exception as error:
+                    print("An exception occurred while getting slow5 end_reason:", type(error).__name__, "-", error)
+                    print("slow5_end_reason_labels: {}".format(slow5_end_reason_labels))
+                    sys.exit(1)
                 reason, forced = s2p_end_reason_convert(s5_end_reason)
                 end_reason = p5.EndReason(reason=reason, forced=forced)
 
@@ -941,6 +951,11 @@ def m2s_s2p_worker(args, slow5_filepath_set, pod5_out):
                 slow5_end_reason_labels = s5.get_aux_enum_labels("end_reason")
             except:
                 slow5_end_reason_labels = ['unknown']
+
+            # if the above fails, it goes to unknown, but if it doesn't exist, it returns and empty list
+            # so let's set it to unknown
+            if len(slow5_end_reason_labels) < 1:
+                slow5_end_reason_labels = ['unknown']
             # before ONT added DATA_SERVICE_UNBLOCK_MUX_CHANGE in the middle and removed partial...
             # slow5_end_reason_labels = ['unknown', 'partial', 'mux_change', 'unblock_mux_change', 'signal_positive', 'signal_negative']
             for read in reads:
@@ -962,7 +977,12 @@ def m2s_s2p_worker(args, slow5_filepath_set, pod5_out):
                 # sampling_frequency = read["sampling_rate"]
                 # map end_reason if present
                 # let's convert this to it's string equivalent
-                s5_end_reason = slow5_end_reason_labels[read.get("end_reason", 0)]
+                try:
+                    s5_end_reason = slow5_end_reason_labels[read.get("end_reason", 0)]
+                except Exception as error:
+                    print("An exception occurred while getting slow5 end_reason:", type(error).__name__, "-", error)
+                    print("slow5_end_reason_labels: {}".format(slow5_end_reason_labels))
+                    sys.exit(1)
                 reason, forced = s2p_end_reason_convert(s5_end_reason)
                 end_reason = p5.EndReason(reason=reason, forced=forced)
 
@@ -1135,6 +1155,10 @@ def s2s_s2p_worker(args, sfile, pod5_out):
         slow5_end_reason_labels = s5.get_aux_enum_labels("end_reason")
     except:
         slow5_end_reason_labels = ['unknown']
+    # if the above fails, it goes to unknown, but if it doesn't exist, it returns and empty list
+    # so let's set it to unknown
+    if len(slow5_end_reason_labels) < 1:
+        slow5_end_reason_labels = ['unknown']
     run_info_cache = {}
     # before ONT added DATA_SERVICE_UNBLOCK_MUX_CHANGE in the middle and removed partial...
     # slow5_end_reason_labels = ['unknown', 'partial', 'mux_change', 'unblock_mux_change', 'signal_positive', 'signal_negative']
@@ -1158,7 +1182,12 @@ def s2s_s2p_worker(args, sfile, pod5_out):
             # sampling_frequency = read["sampling_rate"]
             # map end_reason if present
             # let's convert this to it's string equivalent
-            s5_end_reason = slow5_end_reason_labels[read.get("end_reason", 0)]
+            try:
+                s5_end_reason = slow5_end_reason_labels[read.get("end_reason", 0)]
+            except Exception as error:
+                print("An exception occurred while getting slow5 end_reason:", type(error).__name__, "-", error)
+                print("slow5_end_reason_labels: {}".format(slow5_end_reason_labels))
+                sys.exit(1)
             reason, forced = s2p_end_reason_convert(s5_end_reason)
             end_reason = p5.EndReason(reason=reason, forced=forced)
 
@@ -1368,7 +1397,7 @@ def main():
 
     parser = MyParser(description="SLOW5/BLOW5 <-> POD5 converter",
     epilog='''
-See https://slow5.page.link/blue-crab for detailed description of these command-line options.
+See https://slow5.bioinf.science/blue-crab for detailed description of these command-line options.
 
 Citation:
 Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al. Fast nanopore sequencing data analysis with SLOW5. Nat Biotechnol 40, 1026-1029 (2022). https://doi.org/10.1038/s41587-021-01147-4

diff --git a/test/test_extensive.sh b/test/test_extensive.sh
@@ -51,7 +51,7 @@ slow5tools --version > /dev/null || die "slow5tools not in path"
 
 echo "********************************zymo****************************************"
 DATA_ZYMO=/data/jamfer/zymo/
-test -d $DATA_ZYMO || die "ERROR: $DATA_ZYMO not found. Download from https://slow5.page.link/na12878_prom_sub and extract"
+test -d $DATA_ZYMO || die "ERROR: $DATA_ZYMO not found. Download from https://slow5.bioinf.science/na12878_prom_sub and extract"
 mkdir $TMP_DIR || die "Creating $TMP_DIR failed"
 test/test_with_guppy.sh $DATA_ZYMO/pod5 $TMP_DIR slow5tools /install/ont-guppy-6.5.7/bin/guppy_basecaller blue-crab &> test_s2p_with_guppy_sub.log || die "test_s2p_with_guppy failed"
 rm -r $TMP_DIR