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#################################################################
# Importing samtools, bcftools, and htslib
#
# For each package PKG:
#
# rm -rf PKG
# python import.py PKG path/to/download/PKG-X.Y
import fnmatch
import os
from pathlib import Path
import re
import itertools
import shutil
import sys
import hashlib
EXCLUDE = {
"samtools": (
"test", "misc",
"bgzip.c",
"main.c",
"calDepth.c",
"bam2bed.c",
"bam_tview.c",
"bam_tview.h",
"bam_tview_html.c",
"bam_tview_curses.c",
"bam2bcf.c",
"bam2bcf.h",
"vcf-miniview.c",
),
"bcftools": (
"test", "plugins", "peakfit.c",
"peakfit.h",
"polysomy.c"),
"htslib": (
'annot-tsv.c', 'bgzip.c', 'htsfile.c', 'tabix.c',
'hts_probe_cc.sh',
"samples", "test", "tests"),
}
MAIN = {
"samtools": "bamtk",
"bcftools": "main"
}
C_VERSION = {
"htslib": "HTS_VERSION_TEXT",
"samtools": "SAMTOOLS_VERSION",
"bcftools": "BCFTOOLS_VERSION"
}
def locate(pattern, root=os.curdir, exclude=[], exclude_htslib=False):
'''Locate all files matching supplied filename pattern (but not listed
in exclude) in and below the supplied root directory. Omit any files under
directories listed in exclude or (if exclude_htslib=True) matching /htslib-*/.
'''
for path, dirs, files in os.walk(os.path.abspath(root)):
for filename in fnmatch.filter(files, pattern):
if filename not in exclude:
yield os.path.join(path, filename)
for dirname in exclude:
if dirname in dirs: dirs.remove(dirname)
if exclude_htslib:
for dirname in [d for d in dirs if re.match(r"htslib-", d)]:
dirs.remove(dirname)
def _update_pysam_files(cf, destdir):
'''update pysam files applying redirection of ouput'''
basename = os.path.basename(destdir)
for filename in cf:
if not filename:
continue
dest = filename + ".pysam.c"
with open(filename, encoding="utf-8") as infile:
lines = "".join(infile.readlines())
with open(dest, "w", encoding="utf-8") as outfile:
outfile.write('#include "{}.pysam.h"\n\n'.format(basename))
subname, _ = os.path.splitext(os.path.basename(filename))
if subname in MAIN.get(basename, []):
lines = re.sub(r"int main\(", "int {}_main(".format(
basename), lines)
else:
lines = re.sub(r"int main\(", "int {}_{}_main(".format(
basename, subname), lines)
lines = re.sub(r"\b({}_stdout)\b".format(basename), r"\1_internal", lines)
lines = re.sub(r"\bexit\(", "{}_exit(".format(basename), lines)
lines = re.sub(r"\bstderr\b", "{}_stderr".format(basename), lines)
lines = re.sub(r"\bstdout\b", "{}_stdout".format(basename), lines)
lines = re.sub(r" printf\(", " fprintf({}_stdout, ".format(basename), lines)
lines = re.sub(r"([^kf])puts\(", r"\1{}_puts(".format(basename), lines)
lines = re.sub(r"putchar\(([^)]+)\)",
r"fputc(\1, {}_stdout)".format(basename), lines)
fn = os.path.basename(filename)
# some specific fixes:
SPECIFIC_SUBSTITUTIONS = {
"bam_md.c": (
'sam_open_format("-", mode_w',
'sam_open_format({}_stdout_fn, mode_w'.format(basename)),
"phase.c": (
'putc("ACGT"[f->seq[j] == 1? (c&3, {}_stdout) : (c>>16&3)]);'.format(basename),
'putc("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)], {}_stdout);'.format(basename)),
"cut_target.c": (
'putc(33 + (cns[j]>>8>>2, {}_stdout));'.format(basename),
'putc(33 + (cns[j]>>8>>2), {}_stdout);'.format(basename))
}
if fn in SPECIFIC_SUBSTITUTIONS:
lines = lines.replace(
SPECIFIC_SUBSTITUTIONS[fn][0],
SPECIFIC_SUBSTITUTIONS[fn][1])
if fn == "bamtk.c":
lines = re.sub(r'(#include "version.h")', r'\1\n#include "samtools_config_vars.h"', lines)
lines = re.sub(r'(else if.*"tview")', r'//\1', lines)
lines = re.sub(r'(if[ (]*fclose)', r'if (0) { //\1', lines)
outfile.write(lines)
with open(os.path.join("import", "pysam.h")) as inf, \
open(os.path.join(destdir, "{}.pysam.h".format(basename)), "w") as outf:
outf.write(re.sub("@pysam@", basename, inf.read()))
with open(os.path.join("import", "pysam.c")) as inf, \
open(os.path.join(destdir, "{}.pysam.c".format(basename)), "w") as outf:
outf.write(re.sub("@pysam@", basename, inf.read()))
if len(sys.argv) >= 1:
if len(sys.argv) != 3:
raise ValueError("import requires dest src")
dest, srcdir = sys.argv[1:3]
if dest not in EXCLUDE:
raise ValueError("import expected one of %s" %
",".join(EXCLUDE.keys()))
exclude = EXCLUDE[dest]
destdir = os.path.abspath(dest)
srcdir = os.path.abspath(srcdir)
if not os.path.exists(srcdir):
raise IOError(
"source directory `%s` does not exist." % srcdir)
cfiles = locate("*.c", srcdir, exclude=exclude, exclude_htslib=True)
hfiles = locate("*.h", srcdir, exclude=exclude, exclude_htslib=True)
mfiles = itertools.chain(locate("README", srcdir), locate("LICENSE", srcdir),
locate("version.sh", srcdir, exclude_htslib=True))
if dest == "htslib":
# Add build files, including *.ac config.{guess,sub} *.in *.mk *.m4 *.sh
mfiles = itertools.chain(mfiles, locate("Makefile", srcdir),
locate("configure", srcdir),
locate("config.*", srcdir),
locate("*.[aims][cnk4h]", srcdir, exclude))
ncopied = 0
def _compareAndCopy(src, srcdir, destdir, exclude):
d, f = os.path.split(src)
common_prefix = os.path.commonprefix((d, srcdir))
subdir = re.sub(common_prefix, "", d)[1:]
targetdir = os.path.join(destdir, subdir)
if not os.path.exists(targetdir):
os.makedirs(targetdir)
old_file = os.path.join(targetdir, f)
if os.path.exists(old_file):
md5_old = hashlib.md5(
"".join(open(old_file, "r", encoding="utf-8").readlines()).encode()).digest()
md5_new = hashlib.md5(
"".join(open(src, "r", encoding="utf-8").readlines()).encode()).digest()
if md5_old != md5_new:
raise ValueError(
"incompatible files for %s and %s" %
(old_file, src))
shutil.copy(src, targetdir)
return old_file
for src_file in hfiles:
_compareAndCopy(src_file, srcdir, destdir, exclude)
ncopied += 1
for src_file in mfiles:
_compareAndCopy(src_file, srcdir, destdir, exclude)
ncopied += 1
cf = []
for src_file in cfiles:
cf.append(_compareAndCopy(src_file,
srcdir,
destdir,
exclude))
ncopied += 1
sys.stdout.write(
"installed latest source code from %s: "
"%i files copied\n" % (srcdir, ncopied))
if dest in MAIN:
# redirect stderr to pysamerr and replace bam.h with a stub.
sys.stdout.write("applying stderr redirection\n")
_update_pysam_files(cf, destdir)
def _getVersion(srcdir):
with open(os.path.join(srcdir, "version.sh"), encoding="utf-8") as inf:
for line in inf:
m = re.match(r"VERSION=(\S+)", line)
if m: return m.group(1)
raise ValueError("no VERSION line in version.sh")
def _update_version_file(key, value, filename):
tmpfilename = filename + ".tmp"
with open(filename, encoding="utf-8") as inf:
with open(tmpfilename, "w", encoding="utf-8") as outf:
for line in inf:
if key in line:
line = re.sub(r'"[^"]*"', '"{}"'.format(value), line)
outf.write(line)
os.rename(tmpfilename, filename)
def _update_version_doc_file(dest, value, filename):
tmpfilename = filename + ".tmp"
with open(filename, encoding="utf-8") as inf:
with open(tmpfilename, "w", encoding="utf-8") as outf:
for line in inf:
if " wraps " in line:
# hide the sentence's fullstop from the main regexp
line = re.sub(r'\.$', ',DOT', line)
line = re.sub(r'{}-[^*,]*'.format(dest),
'{}-{}'.format(dest, value), line)
line = re.sub(',DOT', '.', line)
outf.write(line)
os.rename(tmpfilename, filename)
version = _getVersion(srcdir)
_update_version_file("__{}_version__".format(dest), version, "pysam/version.py")
_update_version_file(C_VERSION[dest], version + " (pysam)", "pysam/version.h")
_update_version_doc_file(dest, version, "README.rst")
_update_version_doc_file(dest, version, "doc/index.rst")
if dest in MAIN:
path = Path("doc/conf.py")
path.write_text(re.sub(rf"doc/[\d.]*/{dest}", rf"doc/{version}/{dest}", path.read_text()))
sys.exit(0)
# if len(sys.argv) >= 2 and sys.argv[1] == "refresh":
# sys.stdout.write("refreshing latest source code from .c to .pysam.c")
# # redirect stderr to pysamerr and replace bam.h with a stub.
# sys.stdout.write("applying stderr redirection")
# for destdir in ('samtools', ):
# pysamcfiles = locate("*.pysam.c", destdir)
# for f in pysamcfiles:
# os.remove(f)
# cfiles = locate("*.c", destdir)
# _update_pysam_files(cfiles, destdir)
# sys.exit(0)
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