gwaslab 3.4.40__tar.gz → 3.4.42__tar.gz

{gwaslab-3.4.40/src/gwaslab.egg-info → gwaslab-3.4.42}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.40
+Version: 3.4.42
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -25,10 +25,10 @@ Requires-Dist: scikit-allel>=1.3.5
 Requires-Dist: pyensembl==2.2.3
 Requires-Dist: gtfparse==1.3.0
 
-<img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197167760-5f761f5e-5856-4b27-a540-8b9cd90bdadb.png">
-
 # GWASLab
 
+<img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197167760-5f761f5e-5856-4b27-a540-8b9cd90bdadb.png">
+
 ![badge](https://img.shields.io/pypi/v/gwaslab)
 [![Downloads](https://static.pepy.tech/badge/gwaslab)](https://pepy.tech/project/gwaslab)
 ![badge_pip](https://img.shields.io/pypi/dm/gwaslab)
@@ -40,15 +40,19 @@ Requires-Dist: gtfparse==1.3.0
 * Sumstats-specific manipulations are designed as methods of a Python object, `gwaslab.Sumstats`.
 
 Please check GWASLab documentation at [https://cloufield.github.io/gwaslab/](https://cloufield.github.io/gwaslab/)
+
 Note: GWASLab is being updated very frequently for now. I will release the first stable version soon! Please stay tuned.
 
+Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/gwaslab/KnownIssues/](https://cloufield.github.io/gwaslab/KnownIssues/) .
+
 ## Install
 
+### install via pip
+
 ```
-pip install gwaslab==3.4.39
+pip install gwaslab==3.4.41
 ```
 
-
 ```python
 import gwaslab as gl
 # load plink2 output
@@ -78,6 +82,27 @@ mysumstats.plot_mqq()
 ...
 ```
 
+### install in conda environment
+
+Create a Python 3.9 environment and install gwaslab using pip:
+
+```
+conda env create -n gwaslab_test -c conda-forge python=3.9
+conda activate gwaslab
+pip install gwaslab==3.4.41
+```
+
+or create a new environment using yml file [environment_3.4.40.yml](https://github.com/Cloufield/gwaslab/blob/main/environment_3.4.40.yml)
+
+```
+conda env create -n gwaslab -f environment_3.4.40.yml
+```
+
+
+### install using docker
+
+A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+
 ## Functions
 
 ### Loading and Formatting
@@ -176,6 +201,9 @@ dependencies:
 ## Sample Data
 - Sample GWAS data used in GWASLab is obtained from: http://jenger.riken.jp/ (Suzuki, Ken, et al. "Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population." Nature genetics 51.3 (2019): 379-386.).
 
+## Acknowledgement
+
+Thanks to @sup3rgiu, @soumickmj and @gmauro for their contributions to the source codes.
 
 ## Contacts
 * Github: [https://github.com/Cloufield/gwaslab](https://github.com/Cloufield/gwaslab)

{gwaslab-3.4.40 → gwaslab-3.4.42}/README.md

@@ -1,7 +1,7 @@
-<img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197167760-5f761f5e-5856-4b27-a540-8b9cd90bdadb.png">
-
 # GWASLab
 
+<img width="600" alt="image" src="https://user-images.githubusercontent.com/40289485/197167760-5f761f5e-5856-4b27-a540-8b9cd90bdadb.png">
+
 ![badge](https://img.shields.io/pypi/v/gwaslab)
 [![Downloads](https://static.pepy.tech/badge/gwaslab)](https://pepy.tech/project/gwaslab)
 ![badge_pip](https://img.shields.io/pypi/dm/gwaslab)
@@ -13,15 +13,19 @@
 * Sumstats-specific manipulations are designed as methods of a Python object, `gwaslab.Sumstats`.
 
 Please check GWASLab documentation at [https://cloufield.github.io/gwaslab/](https://cloufield.github.io/gwaslab/)
+
 Note: GWASLab is being updated very frequently for now. I will release the first stable version soon! Please stay tuned.
 
+Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/gwaslab/KnownIssues/](https://cloufield.github.io/gwaslab/KnownIssues/) .
+
 ## Install
 
+### install via pip
+
 ```
-pip install gwaslab==3.4.39
+pip install gwaslab==3.4.41
 ```
 
-
 ```python
 import gwaslab as gl
 # load plink2 output
@@ -51,6 +55,27 @@ mysumstats.plot_mqq()
 ...
 ```
 
+### install in conda environment
+
+Create a Python 3.9 environment and install gwaslab using pip:
+
+```
+conda env create -n gwaslab_test -c conda-forge python=3.9
+conda activate gwaslab
+pip install gwaslab==3.4.41
+```
+
+or create a new environment using yml file [environment_3.4.40.yml](https://github.com/Cloufield/gwaslab/blob/main/environment_3.4.40.yml)
+
+```
+conda env create -n gwaslab -f environment_3.4.40.yml
+```
+
+
+### install using docker
+
+A docker file is available [here](https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile) for building local images.
+
 ## Functions
 
 ### Loading and Formatting
@@ -149,6 +174,9 @@ dependencies:
 ## Sample Data
 - Sample GWAS data used in GWASLab is obtained from: http://jenger.riken.jp/ (Suzuki, Ken, et al. "Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population." Nature genetics 51.3 (2019): 379-386.).
 
+## Acknowledgement
+
+Thanks to @sup3rgiu, @soumickmj and @gmauro for their contributions to the source codes.
 
 ## Contacts
 * Github: [https://github.com/Cloufield/gwaslab](https://github.com/Cloufield/gwaslab)

{gwaslab-3.4.40 → gwaslab-3.4.42}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.4.40"
+version = "3.4.42"
 authors = [
   { name="Yunye", email="yunye@gwaslab.com" },
 ]

{gwaslab-3.4.40 → gwaslab-3.4.42}/src/gwaslab/bd_common_data.py

@@ -298,9 +298,22 @@ def gtf_to_protein_coding(gtfpath,log=Log(),verbose=True):
 
     return protein_coding_path
 
+####################################################################################################################   
+# From BioPython: https://github.com/biopython/biopython/blob/c5a6b1374267d769b19c1022b4b45472316e78b4/Bio/Seq.py#L36
+def _maketrans(complement_mapping):
+    """Make a python string translation table.
+
+    Arguments:
+     - complement_mapping - a dictionary.
 
-      
+    Returns a translation table (a bytes object of length 256) for use with
+    the python string's translate method.
 
+    Compatible with lower case and upper case sequences.
+    """
+    keys = "".join(complement_mapping.keys()).encode("ASCII")
+    values = "".join(complement_mapping.values()).encode("ASCII")
+    return bytes.maketrans(keys + keys.lower(), values + values.lower())
         
 ####################################################################################################################   
         

{gwaslab-3.4.40 → gwaslab-3.4.42}/src/gwaslab/bd_get_hapmap3.py

@@ -12,7 +12,7 @@ from gwaslab.qc_fix_sumstats import finished
 #A P-value
 #A signed summary statistic (beta, OR, log odds, Z-score, etc)
 
-def gethapmap3(sumstats,rsid="rsID",chrom="CHR", pos="POS", ea="EA", nea="NEA",build="19", verbose=True, match_allele= True, log=Log()):
+def gethapmap3(sumstats,rsid="rsID",chrom="CHR", pos="POS", ea="EA", nea="NEA",build="19", verbose=True, match_allele= True, how="inner", log=Log()):
     ##start function with col checking##########################################################
     _start_line = "extract HapMap3 SNPs"
     _end_line = "extracting HapMap3 SNPs"
@@ -47,7 +47,7 @@ def gethapmap3(sumstats,rsid="rsID",chrom="CHR", pos="POS", ea="EA", nea="NEA",b
     #rsid    A1      A2      #CHROM  POS
     #rs3094315       G       A       1       752566
     
-    if rsid in sumstats.columns:
+    if rsid in sumstats.columns and how=="inner":
         output = sumstats.loc[sumstats[rsid].isin(hapmap3_ref["rsid"].values),:].copy()
         return output
     
@@ -56,11 +56,15 @@ def gethapmap3(sumstats,rsid="rsID",chrom="CHR", pos="POS", ea="EA", nea="NEA",b
         sumstats   ["chr:pos"] = sumstats[chrom].astype("string")+":"+sumstats[pos].astype("string")
         hapmap3_ref["chr:pos"] = hapmap3_ref["#CHROM"]+":"+hapmap3_ref["POS"]
         hapmap3_ref = hapmap3_ref.rename(columns={"rsid":"rsID"})
-        output = pd.merge(sumstats,hapmap3_ref.loc[:,["chr:pos","rsID"]+additional_cols],left_on="chr:pos",right_on="chr:pos",how="inner",suffixes=('', '_hapmap3')).copy()
+        output = pd.merge(sumstats,hapmap3_ref.loc[:,["chr:pos","rsID"]+additional_cols],left_on="chr:pos",right_on="chr:pos",how=how,suffixes=('', '_hapmap3')).copy()
         if match_allele:
             log.write(" -Checking if alleles are same...")
             is_matched = ((output[ea].astype("string") == output["A1"]) & (output[nea].astype("string") == output["A2"])) \
                             | ((output[ea].astype("string") == output["A2"]) & (output[nea].astype("string") == output["A1"]))
+            if how=="right":
+                is_matched = ((output[ea].astype("string") == output["A1"]) & (output[nea].astype("string") == output["A2"])) \
+                            | ((output[ea].astype("string") == output["A2"]) & (output[nea].astype("string") == output["A1"])) | output[ea].isna()
+
             log.write(" -Variants with macthed alleles: {}".format(sum(is_matched)))
             output = output.loc[is_matched,:]
         output = output.drop(columns=["chr:pos"]+additional_cols)