Subprocesses path for bigwig and bigbed outputs (#125)

* Resolving #124

* adds path_to_binary argument to enable user specification when working in various conda environments

bioframe/io/fileops.py

@@ -5,6 +5,9 @@
 import json
 import io
 
+import os
+import shutil
+
 import numpy as np
 import pandas as pd
 
@@ -488,7 +491,7 @@ def read_bigbed(path, chrom, start=None, end=None, engine="auto"):
  return df
 
 
-def to_bigwig(df, chromsizes, outpath, value_field=None):
+def to_bigwig(df, chromsizes, outpath, value_field=None, path_to_binary=None):
  """
  Save a bedGraph-like dataframe as a binary BigWig track.
 
@@ -504,8 +507,34 @@ def to_bigwig(df, chromsizes, outpath, value_field=None):
  value_field : str, optional
  Select the column label of the data frame to generate the track. Default
  is to use the fourth column.
+ path_to_binary : str, optional
+ Provide system path to the bedGraphToBigWig binary.
 
  """
+
+ if path_to_binary is None:
+ cmd = "bedGraphToBigWig"
+ try:
+ assert shutil.which(cmd) is not None
+ except Exception as e:
+ raise ValueError(
+ "bedGraphToBigWig is not present in the current environment. "
+ "Pass it as 'path_to_binary' parameter to bioframe.to_bigwig or "
+ "install it with, for example, conda install -y -c bioconda ucsc-bedgraphtobigwig "
+ )
+ elif path_to_binary.endswith("bedGraphToBigWig"):
+ if not os.path.isfile(path_to_binary) and os.access(path_to_binary, os.X_OK):
+ raise ValueError(
+ f"bedGraphToBigWig is absent in the provided path or cannot be executed: {path_to_binary}. "
+ )
+ cmd = path_to_binary
+ else:
+ cmd = os.path.join(path_to_binary, "bedGraphToBigWig")
+ if not os.path.isfile(cmd) and os.access(cmd, os.X_OK):
+ raise ValueError(
+ f"bedGraphToBigWig is absent in the provided path or cannot be executed: {path_to_binary}. "
+ )
+
  is_bedgraph = True
  for col in ["chrom", "start", "end"]:
  if col not in df.columns:
@@ -527,7 +556,7 @@ def to_bigwig(df, chromsizes, outpath, value_field=None):
  bg = bg.sort_values(["chrom", "start", "end"])
 
  with tempfile.NamedTemporaryFile(suffix=".bg") as f, tempfile.NamedTemporaryFile(
-  "wt", suffix=".chrom.sizes"
+ "wt", suffix=".chrom.sizes"
  ) as cs:
 
  chromsizes.to_csv(cs, sep="\t", header=False)
@@ -538,14 +567,14 @@ def to_bigwig(df, chromsizes, outpath, value_field=None):
  )
 
  p = subprocess.run(
- ["bedGraphToBigWig", f.name, cs.name, outpath],
+ [cmd, f.name, cs.name, outpath],
  stdout=subprocess.PIPE,
  stderr=subprocess.PIPE,
  )
  return p
 
 
-def to_bigbed(df, chromsizes, outpath, schema="bed6"):
+def to_bigbed(df, chromsizes, outpath, schema="bed6", path_to_binary=None):
  """
  Save a bedGraph-like dataframe as a binary BigWig track.
 
@@ -561,8 +590,34 @@ def to_bigbed(df, chromsizes, outpath, schema="bed6"):
  value_field : str, optional
  Select the column label of the data frame to generate the track. Default
  is to use the fourth column.
+ path_to_binary : str, optional
+ Provide system path to the bedGraphToBigWig binary.
 
  """
+
+ if path_to_binary is None:
+ cmd = "bedToBigBed"
+ try:
+ assert shutil.which(cmd) is not None
+ except Exception as e:
+ raise ValueError(
+ "bedToBigBed is not present in the current environment. "
+ "Pass it as 'path_to_binary' parameter to bioframe.to_bigbed or "
+ "install it with, for example, conda install -y -c bioconda ucsc-bedtobigbed "
+ )
+ elif path_to_binary.endswith("bedToBigBed"):
+ if not os.path.isfile(path_to_binary) and os.access(path_to_binary, os.X_OK):
+ raise ValueError(
+ f"bedToBigBed is absent in the provided path or cannot be executed: {path_to_binary}. "
+ )
+ cmd = path_to_binary
+ else:
+ cmd = os.path.join(path_to_binary, "bedGraphToBigWig")
+ if not os.path.isfile(cmd) and os.access(cmd, os.X_OK):
+ raise ValueError(
+ f"bedToBigBed is absent in the provided path or cannot be executed: {path_to_binary}. "
+ )
+
  is_bed6 = True
  for col in ["chrom", "start", "end", "name", "score", "strand"]:
  if col not in df.columns:
@@ -590,7 +645,7 @@ def to_bigbed(df, chromsizes, outpath, schema="bed6"):
  )
 
  p = subprocess.run(
- ["bedToBigBed", "-type={}".format(schema), f.name, cs.name, outpath],
+ [cmd, "-type={}".format(schema), f.name, cs.name, outpath],
  stdout=subprocess.PIPE,
  stderr=subprocess.PIPE,
  )