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#################################################################
# Importing samtools and htslib
#
# For htslib, simply copy the whole release tar-ball
# into the directory "htslib" and recreate the file version.h
#
# rm -rf htslib
# mv download/htslib htslib
# git checkout -- htslib/version.h
# Edit the file htslib/version.h to set the right version number.
#
# For samtools, type:
# rm -rf samtools
# python import.py samtools download/samtools
#
# Manually, then:
# modify config.h to set compatibility flags
#
# For bcftools, type:
# rm -rf bedtools
# python import.py bedtools download/bedtools
# rm -rf bedtools/test bedtools/plugins
import fnmatch
import os
import re
import shutil
import sys
import hashlib
EXCLUDE = {
"samtools": (
"razip.c", "bgzip.c", "main.c",
"calDepth.c", "bam2bed.c", "wgsim.c",
"md5fa.c", "md5sum-lite.c", "maq2sam.c",
"bamcheck.c", "chk_indel.c", "vcf-miniview.c",
"htslib-1.3", # do not import twice
"hfile_irods.c", # requires irods library
),
"bcftools": (
"test", "plugins", "peakfit.c",
"peakfit.h",
# needs to renamed, name conflict with samtools reheader
"reheader.c",
"polysomy.c"),
"htslib": (
'htslib/tabix.c', 'htslib/bgzip.c',
'htslib/htsfile.c', 'htslib/hfile_irods.c'),
}
MAIN = {
"samtools": "bamtk",
"bcftools": "main"
}
def locate(pattern, root=os.curdir):
'''Locate all files matching supplied filename pattern in and below
supplied root directory.
'''
for path, dirs, files in os.walk(os.path.abspath(root)):
for filename in fnmatch.filter(files, pattern):
yield os.path.join(path, filename)
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) as infile:
lines = "".join(infile.readlines())
with open(dest, "w") as outfile:
outfile.write('#include "pysam.h"\n\n')
subname, _ = os.path.splitext(os.path.basename(filename))
if subname in MAIN.get(basename, []):
lines = re.sub("int main\(", "int {}_main(".format(
basename), lines)
else:
lines = re.sub("int main\(", "int {}_{}_main(".format(
basename, subname), lines)
lines = re.sub("stderr", "pysam_stderr", lines)
lines = re.sub("stdout", "pysam_stdout", lines)
lines = re.sub(" printf\(", " fprintf(pysam_stdout, ", lines)
lines = re.sub("([^kf])puts\(([^)]+)\)",
r"\1fputs(\2, pysam_stdout) & fputc('\\n', pysam_stdout)",
lines)
lines = re.sub("putchar\(([^)]+)\)",
r"fputc(\1, pysam_stdout)", lines)
fn = os.path.basename(filename)
# some specific fixes:
SPECIFIC_SUBSTITUTIONS = {
"bam_md.c": (
'sam_open_format("-", mode_w',
'sam_open_format(pysam_stdout_fn, mode_w'),
"phase.c": (
'putc("ACGT"[f->seq[j] == 1? (c&3, pysam_stdout) : (c>>16&3)]);',
'putc("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)], pysam_stdout);'),
"cut_target.c": (
'putc(33 + (cns[j]>>8>>2, pysam_stdout));',
'putc(33 + (cns[j]>>8>>2), pysam_stdout);')
}
if fn in SPECIFIC_SUBSTITUTIONS:
lines = lines.replace(
SPECIFIC_SUBSTITUTIONS[fn][0],
SPECIFIC_SUBSTITUTIONS[fn][1])
outfile.write(lines)
with open(os.path.join(destdir, "pysam.h"), "w")as outfile:
outfile.write("""#ifndef PYSAM_H
#define PYSAM_H
#include "stdio.h"
extern FILE * pysam_stderr;
extern FILE * pysam_stdout;
extern const char * pysam_stdout_fn;
#endif
""")
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)
hfiles = locate("*.h", srcdir)
# remove unwanted files and htslib subdirectory.
cfiles = [x for x in cfiles if os.path.basename(x) not in exclude
and not re.search("htslib-", x)]
hfiles = [x for x in hfiles if os.path.basename(x) not in exclude
and not re.search("htslib-", x)]
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").readlines())).digest()
md5_new = hashlib.md5(
"".join(open(src, "r").readlines())).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
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))
# redirect stderr to pysamerr and replace bam.h with a stub.
sys.stdout.write("applying stderr redirection\n")
_update_pysam_files(cf, destdir)
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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