From 88a757f38a77dc2ba9a5a7d0a40726cc0bee5fac Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Thu, 23 Jan 2020 15:35:54 -0600
Subject: [PATCH] Added utils.py
---
workflow/scripts/utils.py | 136 ++++++++++++++++++++++++++++++++++++++
1 file changed, 136 insertions(+)
create mode 100644 workflow/scripts/utils.py
diff --git a/workflow/scripts/utils.py b/workflow/scripts/utils.py
new file mode 100644
index 0000000..5e4478e
--- /dev/null
+++ b/workflow/scripts/utils.py
@@ -0,0 +1,136 @@
+#!/usr/bin/env python3
+
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
+'''General utilities.'''
+
+
+import shlex
+import logging
+import subprocess
+import sys
+import os
+
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+logger.propagate = True
+
+
+def run_pipe(steps, outfile=None):
+ from subprocess import Popen, PIPE
+ p = None
+ p_next = None
+ first_step_n = 1
+ last_step_n = len(steps)
+ for n, step in enumerate(steps, start=first_step_n):
+ logger.debug("step %d: %s" % (n, step))
+ if n == first_step_n:
+ if n == last_step_n and outfile: # one-step pipeline with outfile
+ with open(outfile, 'w') as fh:
+ print("one step shlex: %s to file: %s" % (shlex.split(step), outfile))
+ p = Popen(shlex.split(step), stdout=fh)
+ break
+ print("first step shlex to stdout: %s" % (shlex.split(step)))
+
+ p = Popen(shlex.split(step), stdout=PIPE)
+ elif n == last_step_n and outfile: # only treat the last step specially if you're sending stdout to a file
+ with open(outfile, 'w') as fh:
+ print("last step shlex: %s to file: %s" % (shlex.split(step), outfile))
+ p_last = Popen(shlex.split(step), stdin=p.stdout, stdout=fh)
+ p.stdout.close()
+ p = p_last
+ else: # handles intermediate steps and, in the case of a pipe to stdout, the last step
+ print("intermediate step %d shlex to stdout: %s" % (n, shlex.split(step)))
+ p_next = Popen(shlex.split(step), stdin=p.stdout, stdout=PIPE)
+ p.stdout.close()
+ p = p_next
+ out, err = p.communicate()
+ return out, err
+
+
+def block_on(command):
+ process = subprocess.Popen(shlex.split(command), stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
+ for line in iter(process.stdout.readline, b''):
+ sys.stdout.write(line.decode('utf-8'))
+ process.communicate()
+ return process.returncode
+
+
+def strip_extensions(filename, extensions):
+ '''Strips extensions to get basename of file.'''
+
+ basename = filename
+ for extension in extensions:
+ basename = basename.rpartition(extension)[0] or basename
+
+ return basename
+
+
+def count_lines(filename):
+ import mimetypes
+ compressed_mimetypes = [
+ "compress",
+ "bzip2",
+ "gzip"
+ ]
+ mime_type = mimetypes.guess_type(filename)[1]
+ if mime_type in compressed_mimetypes:
+ catcommand = 'gzip -dc'
+ else:
+ catcommand = 'cat'
+ out, err = run_pipe([
+ '%s %s' % (catcommand, filename),
+ 'wc -l'
+ ])
+ return int(out)
+
+
+def rescale_scores(filename, scores_col, new_min=10, new_max=1000):
+ sorted_fn = 'sorted-%s' % (filename)
+ rescaled_fn = 'rescaled-%s' % (filename)
+
+ out, err = run_pipe([
+ 'sort -k %dgr,%dgr %s' % (scores_col, scores_col, filename),
+ r"""awk 'BEGIN{FS="\t";OFS="\t"}{if (NF != 0) print $0}'"""],
+ sorted_fn)
+
+ out, err = run_pipe([
+ 'head -n 1 %s' % (sorted_fn),
+ 'cut -f %s' % (scores_col)])
+ max_score = float(out.strip())
+ logger.info("rescale_scores: max_score = %s", max_score)
+
+ out, err = run_pipe([
+ 'tail -n 1 %s' % (sorted_fn),
+ 'cut -f %s' % (scores_col)])
+ min_score = float(out.strip())
+ logger.info("rescale_scores: min_score = %s", min_score)
+
+ a = min_score
+ b = max_score
+ x = new_min
+ y = new_max
+
+ if min_score == max_score: # give all peaks new_min
+ rescale_formula = "x"
+ else: # n is the unscaled score from scores_col
+ rescale_formula = "((n-a)*(y-x)/(b-a))+x"
+
+ out, err = run_pipe(
+ [
+ 'cat %s' % (sorted_fn),
+ r"""awk 'BEGIN{OFS="\t"}{n=$%d;a=%d;b=%d;x=%d;y=%d}"""
+ % (scores_col, a, b, x, y) +
+ r"""{$%d=int(%s) ; print $0}'"""
+ % (scores_col, rescale_formula)
+ ],
+ rescaled_fn)
+
+ os.remove(sorted_fn)
+
+ return rescaled_fn
--
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