Galaxy |

Changeset 1:8b26adf64adc (2013-11-05)

Previous changeset 0:e6df770c0e58 (2013-07-12)

Commit message:
V2.0.5

modified:
BSseeker2/._AUTHORS
BSseeker2/AUTHORS
BSseeker2/FilterReads.py
BSseeker2/README.md
BSseeker2/RELEASE_NOTES
BSseeker2/bs_align/bs_align_utils.py
BSseeker2/bs_align/bs_pair_end.py
BSseeker2/bs_align/bs_rrbs.py
BSseeker2/bs_align/bs_single_end.py
BSseeker2/bs_align/output.py
BSseeker2/bs_index/wg_build.py
BSseeker2/bs_seeker2-align.py
BSseeker2/bs_seeker2-build.py
BSseeker2/bs_seeker2-call_methylation.py
BSseeker2/bs_utils/__init__.py
BSseeker2/bs_utils/utils.py
BSseeker2/galaxy/__init__.py
BSseeker2/galaxy/bs_seeker2_wrapper.py
BSseeker2/galaxy/bs_seeker2_wrapper.xml

removed:
._BSseeker2
BSseeker2/._FilterReads.py
BSseeker2/._README.md
BSseeker2/._RELEASE_NOTES
BSseeker2/._bs_align
BSseeker2/._bs_index
BSseeker2/._bs_seeker2-align.py
BSseeker2/._bs_seeker2-build.py
BSseeker2/._bs_seeker2-call_methylation.py
BSseeker2/._bs_utils
BSseeker2/._galaxy
BSseeker2/bs_align/.___init__.py
BSseeker2/bs_align/._bs_align_utils.py
BSseeker2/bs_align/._bs_pair_end.py
BSseeker2/bs_align/._bs_rrbs.py
BSseeker2/bs_align/._bs_single_end.py
BSseeker2/bs_align/._output.py
BSseeker2/bs_index/.___init__.py
BSseeker2/bs_index/._rrbs_build.py
BSseeker2/bs_index/._wg_build.py
BSseeker2/bs_utils/.___init__.py
BSseeker2/bs_utils/._utils.py
BSseeker2/galaxy/.___init__.py
BSseeker2/galaxy/._bs_seeker2_wrapper.py
BSseeker2/galaxy/._bs_seeker2_wrapper.xml

diff -r e6df770c0e58 -r 8b26adf64adc ._BSseeker2

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.DS_Store

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._.DS_Store

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._AUTHORS

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._FilterReads.py

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._README.md

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._RELEASE_NOTES

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._bs_align

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._bs_index

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._bs_seeker2-align.py

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._bs_seeker2-build.py

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._bs_seeker2-call_methylation.py

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._bs_utils

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/._galaxy

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/COMMIT_EDITMSG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/COMMIT_EDITMSG Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,1 @@
+V2.0.5

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/HEAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/HEAD Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,1 @@
+ref: refs/heads/master

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/config
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/config Tue Nov 05 01:55:39 2013 -0500

[

@@ -0,0 +1,13 @@
+[core]
+ repositoryformatversion = 0
+ filemode = true
+ bare = false
+ logallrefupdates = true
+ ignorecase = true
+ precomposeunicode = false
+[remote "origin"]
+ url = https://github.com/BSSeeker/BSseeker2.git
+ fetch = +refs/heads/*:refs/remotes/origin/*
+[branch "master"]
+ remote = origin
+ merge = refs/heads/master

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/description
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/description Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,1 @@
+Unnamed repository; edit this file 'description' to name the repository.

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/applypatch-msg.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/applypatch-msg.sample Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,15 @@
+#!/bin/sh
+#
+# An example hook script to check the commit log message taken by
+# applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit. The hook is
+# allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "applypatch-msg".
+
+. git-sh-setup
+test -x "$GIT_DIR/hooks/commit-msg" &&
+ exec "$GIT_DIR/hooks/commit-msg" ${1+"$@"}
+:

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/commit-msg.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/commit-msg.sample Tue Nov 05 01:55:39 2013 -0500

[

@@ -0,0 +1,24 @@
+#!/bin/sh
+#
+# An example hook script to check the commit log message.
+# Called by "git commit" with one argument, the name of the file
+# that has the commit message. The hook should exit with non-zero
+# status after issuing an appropriate message if it wants to stop the
+# commit. The hook is allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "commit-msg".
+
+# Uncomment the below to add a Signed-off-by line to the message.
+# Doing this in a hook is a bad idea in general, but the prepare-commit-msg
+# hook is more suited to it.
+#
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^$.*>$.*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
+
+# This example catches duplicate Signed-off-by lines.
+
+test "" = "$(grep '^Signed-off-by: ' "$1" |
+ sort | uniq -c | sed -e '/^[ ]*1[ ]/d')" || {
+ echo >&2 Duplicate Signed-off-by lines.
+ exit 1
+}

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/post-update.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/post-update.sample Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,8 @@
+#!/bin/sh
+#
+# An example hook script to prepare a packed repository for use over
+# dumb transports.
+#
+# To enable this hook, rename this file to "post-update".
+
+exec git update-server-info

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/pre-applypatch.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/pre-applypatch.sample Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,14 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed
+# by applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-applypatch".
+
+. git-sh-setup
+test -x "$GIT_DIR/hooks/pre-commit" &&
+ exec "$GIT_DIR/hooks/pre-commit" ${1+"$@"}
+:

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/pre-commit.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/pre-commit.sample Tue Nov 05 01:55:39 2013 -0500

[

@@ -0,0 +1,50 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed.
+# Called by "git commit" with no arguments.  The hook should
+# exit with non-zero status after issuing an appropriate message if
+# it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-commit".
+
+if git rev-parse --verify HEAD >/dev/null 2>&1
+then
+ against=HEAD
+else
+ # Initial commit: diff against an empty tree object
+ against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
+fi
+
+# If you want to allow non-ascii filenames set this variable to true.
+allownonascii=$(git config hooks.allownonascii)
+
+# Redirect output to stderr.
+exec 1>&2
+
+# Cross platform projects tend to avoid non-ascii filenames; prevent
+# them from being added to the repository. We exploit the fact that the
+# printable range starts at the space character and ends with tilde.
+if [ "$allownonascii" != "true" ] &&
+ # Note that the use of brackets around a tr range is ok here, (it's
+ # even required, for portability to Solaris 10's /usr/bin/tr), since
+ # the square bracket bytes happen to fall in the designated range.
+ test $(git diff --cached --name-only --diff-filter=A -z $against |
+   LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
+then
+ echo "Error: Attempt to add a non-ascii file name."
+ echo
+ echo "This can cause problems if you want to work"
+ echo "with people on other platforms."
+ echo
+ echo "To be portable it is advisable to rename the file ..."
+ echo
+ echo "If you know what you are doing you can disable this"
+ echo "check using:"
+ echo
+ echo "  git config hooks.allownonascii true"
+ echo
+ exit 1
+fi
+
+# If there are whitespace errors, print the offending file names and fail.
+exec git diff-index --check --cached $against --

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/pre-push.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/pre-push.sample Tue Nov 05 01:55:39 2013 -0500

[

@@ -0,0 +1,53 @@
+#!/bin/sh
+
+# An example hook script to verify what is about to be pushed.  Called by "git
+# push" after it has checked the remote status, but before anything has been
+# pushed.  If this script exits with a non-zero status nothing will be pushed.
+#
+# This hook is called with the following parameters:
+#
+# $1 -- Name of the remote to which the push is being done
+# $2 -- URL to which the push is being done
+#
+# If pushing without using a named remote those arguments will be equal.
+#
+# Information about the commits which are being pushed is supplied as lines to
+# the standard input in the form:
+#
+#   <local ref> <local sha1> <remote ref> <remote sha1>
+#
+# This sample shows how to prevent push of commits where the log message starts
+# with "WIP" (work in progress).
+
+remote="$1"
+url="$2"
+
+z40=0000000000000000000000000000000000000000
+
+IFS=' '
+while read local_ref local_sha remote_ref remote_sha
+do
+ if [ "$local_sha" = $z40 ]
+ then
+ # Handle delete
+ else
+ if [ "$remote_sha" = $z40 ]
+ then
+ # New branch, examine all commits
+ range="$local_sha"
+ else
+ # Update to existing branch, examine new commits
+ range="$remote_sha..$local_sha"
+ fi
+
+ # Check for WIP commit
+ commit=`git rev-list -n 1 --grep '^WIP' "$range"`
+ if [ -n "$commit" ]
+ then
+ echo "Found WIP commit in $local_ref, not pushing"
+ exit 1
+ fi
+ fi
+done
+
+exit 0

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/pre-rebase.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/pre-rebase.sample Tue Nov 05 01:55:39 2013 -0500

[

@@ -0,0 +1,169 @@
+#!/bin/sh
+#
+# Copyright (c) 2006, 2008 Junio C Hamano
+#
+# The "pre-rebase" hook is run just before "git rebase" starts doing
+# its job, and can prevent the command from running by exiting with
+# non-zero status.
+#
+# The hook is called with the following parameters:
+#
+# $1 -- the upstream the series was forked from.
+# $2 -- the branch being rebased (or empty when rebasing the current branch).
+#
+# This sample shows how to prevent topic branches that are already
+# merged to 'next' branch from getting rebased, because allowing it
+# would result in rebasing already published history.
+
+publish=next
+basebranch="$1"
+if test "$#" = 2
+then
+ topic="refs/heads/$2"
+else
+ topic=`git symbolic-ref HEAD` ||
+ exit 0 ;# we do not interrupt rebasing detached HEAD
+fi
+
+case "$topic" in
+refs/heads/??/*)
+ ;;
+*)
+ exit 0 ;# we do not interrupt others.
+ ;;
+esac
+
+# Now we are dealing with a topic branch being rebased
+# on top of master.  Is it OK to rebase it?
+
+# Does the topic really exist?
+git show-ref -q "$topic" || {
+ echo >&2 "No such branch $topic"
+ exit 1
+}
+
+# Is topic fully merged to master?
+not_in_master=`git rev-list --pretty=oneline ^master "$topic"`
+if test -z "$not_in_master"
+then
+ echo >&2 "$topic is fully merged to master; better remove it."
+ exit 1 ;# we could allow it, but there is no point.
+fi
+
+# Is topic ever merged to next?  If so you should not be rebasing it.
+only_next_1=`git rev-list ^master "^$topic" ${publish} | sort`
+only_next_2=`git rev-list ^master           ${publish} | sort`
+if test "$only_next_1" = "$only_next_2"
+then
+ not_in_topic=`git rev-list "^$topic" master`
+ if test -z "$not_in_topic"
+ then
+ echo >&2 "$topic is already up-to-date with master"
+ exit 1 ;# we could allow it, but there is no point.
+ else
+ exit 0
+ fi
+else
+ not_in_next=`git rev-list --pretty=oneline ^${publish} "$topic"`
+ /usr/bin/perl -e '
+ my $topic = $ARGV[0];
+ my $msg = "* $topic has commits already merged to public branch:\n";
+ my (%not_in_next) = map {
+ /^([0-9a-f]+) /;
+ ($1 => 1);
+ } split(/\n/, $ARGV[1]);
+ for my $elem (map {
+ /^([0-9a-f]+) (.*)$/;
+ [$1 => $2];
+ } split(/\n/, $ARGV[2])) {
+ if (!exists $not_in_next{$elem->[0]}) {
+ if ($msg) {
+ print STDERR $msg;
+ undef $msg;
+ }
+ print STDERR " $elem->[1]\n";
+ }
+ }
+ ' "$topic" "$not_in_next" "$not_in_master"
+ exit 1
+fi
+
+exit 0
+
+################################################################
+
+This sample hook safeguards topic branches that have been
+published from being rewound.
+
+The workflow assumed here is:
+
+ * Once a topic branch forks from "master", "master" is never
+   merged into it again (either directly or indirectly).
+
+ * Once a topic branch is fully cooked and merged into "master",
+   it is deleted.  If you need to build on top of it to correct
+   earlier mistakes, a new topic branch is created by forking at
+   the tip of the "master".  This is not strictly necessary, but
+   it makes it easier to keep your history simple.
+
+ * Whenever you need to test or publish your changes to topic
+   branches, merge them into "next" branch.
+
+The script, being an example, hardcodes the publish branch name
+to be "next", but it is trivial to make it configurable via
+$GIT_DIR/config mechanism.
+
+With this workflow, you would want to know:
+
+(1) ... if a topic branch has ever been merged to "next".  Young
+    topic branches can have stupid mistakes you would rather
+    clean up before publishing, and things that have not been
+    merged into other branches can be easily rebased without
+    affecting other people.  But once it is published, you would
+    not want to rewind it.
+
+(2) ... if a topic branch has been fully merged to "master".
+    Then you can delete it.  More importantly, you should not
+    build on top of it -- other people may already want to
+    change things related to the topic as patches against your
+    "master", so if you need further changes, it is better to
+    fork the topic (perhaps with the same name) afresh from the
+    tip of "master".
+
+Let's look at this example:
+
+    o---o---o---o---o---o---o---o---o---o "next"
+   /       /           /           /
+ /   a---a---b A     /           /
+ /   /               /           /
+        /   /   c---c---c---c B         /
+       /   /   /             \         /
+      /   /   /   b---b C     \       /
+     /   /   /   /             \     /
+    ---o---o---o---o---o---o---o---o---o---o---o "master"
+
+
+A, B and C are topic branches.
+
+ * A has one fix since it was merged up to "next".
+
+ * B has finished.  It has been fully merged up to "master" and "next",
+   and is ready to be deleted.
+
+ * C has not merged to "next" at all.
+
+We would want to allow C to be rebased, refuse A, and encourage
+B to be deleted.
+
+To compute (1):
+
+ git rev-list ^master ^topic next
+ git rev-list ^master        next
+
+ if these match, topic has not merged in next at all.
+
+To compute (2):
+
+ git rev-list master..topic
+
+ if this is empty, it is fully merged to "master".

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/prepare-commit-msg.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/prepare-commit-msg.sample Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,36 @@
+#!/bin/sh
+#
+# An example hook script to prepare the commit log message.
+# Called by "git commit" with the name of the file that has the
+# commit message, followed by the description of the commit
+# message's source.  The hook's purpose is to edit the commit
+# message file.  If the hook fails with a non-zero status,
+# the commit is aborted.
+#
+# To enable this hook, rename this file to "prepare-commit-msg".
+
+# This hook includes three examples.  The first comments out the
+# "Conflicts:" part of a merge commit.
+#
+# The second includes the output of "git diff --name-status -r"
+# into the message, just before the "git status" output.  It is
+# commented because it doesn't cope with --amend or with squashed
+# commits.
+#
+# The third example adds a Signed-off-by line to the message, that can
+# still be edited.  This is rarely a good idea.
+
+case "$2,$3" in
+  merge,)
+    /usr/bin/perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;;
+
+# ,|template,)
+#   /usr/bin/perl -i.bak -pe '
+#      print "\n" . `git diff --cached --name-status -r`
+# if /^#/ && $first++ == 0' "$1" ;;
+
+  *) ;;
+esac
+
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^$.*>$.*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/hooks/update.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/hooks/update.sample Tue Nov 05 01:55:39 2013 -0500

[

@@ -0,0 +1,128 @@
+#!/bin/sh
+#
+# An example hook script to blocks unannotated tags from entering.
+# Called by "git receive-pack" with arguments: refname sha1-old sha1-new
+#
+# To enable this hook, rename this file to "update".
+#
+# Config
+# ------
+# hooks.allowunannotated
+#   This boolean sets whether unannotated tags will be allowed into the
+#   repository.  By default they won't be.
+# hooks.allowdeletetag
+#   This boolean sets whether deleting tags will be allowed in the
+#   repository.  By default they won't be.
+# hooks.allowmodifytag
+#   This boolean sets whether a tag may be modified after creation. By default
+#   it won't be.
+# hooks.allowdeletebranch
+#   This boolean sets whether deleting branches will be allowed in the
+#   repository.  By default they won't be.
+# hooks.denycreatebranch
+#   This boolean sets whether remotely creating branches will be denied
+#   in the repository.  By default this is allowed.
+#
+
+# --- Command line
+refname="$1"
+oldrev="$2"
+newrev="$3"
+
+# --- Safety check
+if [ -z "$GIT_DIR" ]; then
+ echo "Don't run this script from the command line." >&2
+ echo " (if you want, you could supply GIT_DIR then run" >&2
+ echo "  $0 <ref> <oldrev> <newrev>)" >&2
+ exit 1
+fi
+
+if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
+ echo "Usage: $0 <ref> <oldrev> <newrev>" >&2
+ exit 1
+fi
+
+# --- Config
+allowunannotated=$(git config --bool hooks.allowunannotated)
+allowdeletebranch=$(git config --bool hooks.allowdeletebranch)
+denycreatebranch=$(git config --bool hooks.denycreatebranch)
+allowdeletetag=$(git config --bool hooks.allowdeletetag)
+allowmodifytag=$(git config --bool hooks.allowmodifytag)
+
+# check for no description
+projectdesc=$(sed -e '1q' "$GIT_DIR/description")
+case "$projectdesc" in
+"Unnamed repository"* | "")
+ echo "*** Project description file hasn't been set" >&2
+ exit 1
+ ;;
+esac
+
+# --- Check types
+# if $newrev is 0000...0000, it's a commit to delete a ref.
+zero="0000000000000000000000000000000000000000"
+if [ "$newrev" = "$zero" ]; then
+ newrev_type=delete
+else
+ newrev_type=$(git cat-file -t $newrev)
+fi
+
+case "$refname","$newrev_type" in
+ refs/tags/*,commit)
+ # un-annotated tag
+ short_refname=${refname##refs/tags/}
+ if [ "$allowunannotated" != "true" ]; then
+ echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
+ echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
+ exit 1
+ fi
+ ;;
+ refs/tags/*,delete)
+ # delete tag
+ if [ "$allowdeletetag" != "true" ]; then
+ echo "*** Deleting a tag is not allowed in this repository" >&2
+ exit 1
+ fi
+ ;;
+ refs/tags/*,tag)
+ # annotated tag
+ if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1
+ then
+ echo "*** Tag '$refname' already exists." >&2
+ echo "*** Modifying a tag is not allowed in this repository." >&2
+ exit 1
+ fi
+ ;;
+ refs/heads/*,commit)
+ # branch
+ if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then
+ echo "*** Creating a branch is not allowed in this repository" >&2
+ exit 1
+ fi
+ ;;
+ refs/heads/*,delete)
+ # delete branch
+ if [ "$allowdeletebranch" != "true" ]; then
+ echo "*** Deleting a branch is not allowed in this repository" >&2
+ exit 1
+ fi
+ ;;
+ refs/remotes/*,commit)
+ # tracking branch
+ ;;
+ refs/remotes/*,delete)
+ # delete tracking branch
+ if [ "$allowdeletebranch" != "true" ]; then
+ echo "*** Deleting a tracking branch is not allowed in this repository" >&2
+ exit 1
+ fi
+ ;;
+ *)
+ # Anything else (is there anything else?)
+ echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
+ exit 1
+ ;;
+esac
+
+# --- Finished
+exit 0

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/index

Binary file BSseeker2/.git/index has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/info/exclude
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/info/exclude Tue Nov 05 01:55:39 2013 -0500

[

@@ -0,0 +1,7 @@
+# git ls-files --others --exclude-from=.git/info/exclude
+# Lines that start with '#' are comments.
+# For a project mostly in C, the following would be a good set of
+# exclude patterns (uncomment them if you want to use them):
+# *.[oa]
+# *~
+.DS_Store

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/logs/HEAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/logs/HEAD Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,17 @@
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+203e3ea9ba50c325d53e45f6d31686b6b23bba41 6aeb6fc0a2180cd14c59d772e05c4c3139f37f2e weilong <guoweilong@gmail.com> 1368872339 -0700 commit: Clean-up/Galaxy/Test_data
+6aeb6fc0a2180cd14c59d772e05c4c3139f37f2e 4a0fe7b0dfa14e5b4b62b5ead7a624f7361fee12 weilong <guoweilong@gmail.com> 1368872394 -0700 commit: Clean-up/galaxy/test_data
+4a0fe7b0dfa14e5b4b62b5ead7a624f7361fee12 3544b8bb1e5666d100f7652fc63b985187990e49 weilong <guoweilong@gmail.com> 1369030442 -0700 commit: Fix bug on utils.py; Increased version; Add UPDATE
+3544b8bb1e5666d100f7652fc63b985187990e49 39508bee8506ce06feead7599a53ffd09cc89198 weilong <guoweilong@gmail.com> 1369355033 -0700 commit: support diff indexes
+39508bee8506ce06feead7599a53ffd09cc89198 99e2633f8338b3c1f44cf3d1e2fa7ed5e3ce73ed weilong <guoweilong@gmail.com> 1369785459 -0700 commit: Update Readme
+99e2633f8338b3c1f44cf3d1e2fa7ed5e3ce73ed 823880bb2ebba5ae6bd1c7de7dfc4ce03935155b weilong <guoweilong@gmail.com> 1369876356 -0700 commit: fix bug in galaxy; chmod +x *.py
+823880bb2ebba5ae6bd1c7de7dfc4ce03935155b 7664a927ba6f12b023f6cd72dc407e616c5b85e5 weilong <guoweilong@gmail.com> 1370044685 -0700 commit: fix galaxy xml
+7664a927ba6f12b023f6cd72dc407e616c5b85e5 3c14c7a6fc9fd01ef7ffc3bc3b16153e20fda931 weilong <guoweilong@gmail.com> 1371202921 -0700 commit: fix bugs for RRBS tag
+3c14c7a6fc9fd01ef7ffc3bc3b16153e20fda931 58de749ac6ebe90f32db2c89cdd72507669695e2 weilong <guoweilong@gmail.com> 1371366774 -0700 commit: fix bugs for RRBS tag
+58de749ac6ebe90f32db2c89cdd72507669695e2 5ffa6c0f3f3d1b78e2899cc1ad9636affb5f2330 weilong <guoweilong@gmail.com> 1375139287 -0700 commit: v2.0.4
+5ffa6c0f3f3d1b78e2899cc1ad9636affb5f2330 0c877f0900535fbee6909dc1591e8ad0eac29c52 weilong <guoweilong@gmail.com> 1375307754 -0700 commit: fix a bug
+0c877f0900535fbee6909dc1591e8ad0eac29c52 85a936d6dab3f3c5585bcab2eee7b18bbc7d7fd8 weilong <guoweilong@gmail.com> 1383633776 +0800 commit: V2.0.5

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/logs/refs/heads/master
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/logs/refs/heads/master Tue Nov 05 01:55:39 2013 -0500

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/logs/refs/remotes/origin/HEAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/logs/refs/remotes/origin/HEAD Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,1 @@
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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/logs/refs/remotes/origin/master
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/logs/refs/remotes/origin/master Tue Nov 05 01:55:39 2013 -0500

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+565f548bc9a4ffcad63323481e8b03cb78a84b0a 1373f3c499ff4b6fb8ddff39e8859fa5326d0098 weilong <guoweilong@gmail.com> 1366217075 -0700 push: fast forward
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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/packed-refs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/packed-refs Tue Nov 05 01:55:39 2013 -0500

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+6d252c627030a29eff9cc938f74c0be27ec853f0 refs/remotes/origin/master

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/refs/heads/master
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/refs/remotes/origin/HEAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/refs/remotes/origin/HEAD Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,1 @@
+ref: refs/remotes/origin/master

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.git/refs/remotes/origin/master
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.git/refs/remotes/origin/master Tue Nov 05 01:55:39 2013 -0500

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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/.name
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/.name Tue Nov 05 01:55:39 2013 -0500

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+BSseeker2
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/BSseeker2.iml Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
+

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/encodings.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/encodings.xml Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false" />
+</project>
+

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/misc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/misc.xml Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectRootManager" version="2" project-jdk-name="Python 2.7.2 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python)" project-jdk-type="Python SDK" />
+</project>
+

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/modules.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/modules.xml Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/BSseeker2.iml" filepath="$PROJECT_DIR$/.idea/BSseeker2.iml" />
+    </modules>
+  </component>
+</project>
+

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/other.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/other.xml Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="PyDocumentationSettings">
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+</project>
+

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/scopes/scope_settings.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/scopes/scope_settings.xml Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,5 @@
+<component name="DependencyValidationManager">
+  <state>
+    <option name="SKIP_IMPORT_STATEMENTS" value="false" />
+  </state>
+</component>
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diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/testrunner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/testrunner.xml Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="TestRunnerService">
+    <option name="projectConfiguration" value="Unittests" />
+    <option name="PROJECT_TEST_RUNNER" value="Unittests" />
+  </component>
+</project>
+

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/vcs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/vcs.xml Tue Nov 05 01:55:39 2013 -0500

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
+

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/.idea/workspace.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/.idea/workspace.xml Tue Nov 05 01:55:39 2013 -0500

b'@@ -0,0 +1,644 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<project version="4">\n+ <component name="ChangeListManager">\n+ <list default="true" id="172bd281-b8c2-4544-b510-26029a6498b7" name="Default" comment="" />\n+ <ignored path="BSseeker2.iws" />\n+ <ignored path=".idea/workspace.xml" />\n+ <file path="/Dummy.txt" changelist="172bd281-b8c2-4544-b510-26029a6498b7" time="1383633767371" ignored="false" />\n+ <file path="/a.py" changelist="172bd281-b8c2-4544-b510-26029a6498b7" time="1365491538292" ignored="false" />\n+ <file path="/bs_rrbs.py" changelist="172bd281-b8c2-4544-b510-26029a6498b7" time="1383621399873" ignored="false" />\n+ <file path="/bs_pair_end.py" changelist="172bd281-b8c2-4544-b510-26029a6498b7" time="1383622148043" ignored="false" />\n+ <file path="/bs_single_end.py" changelist="172bd281-b8c2-4544-b510-26029a6498b7" time="1383571511133" ignored="false" />\n+ <file path="/bs_align_utils.py" changelist="172bd281-b8c2-4544-b510-26029a6498b7" time="1381998901080" 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<provider selected="true" editor-type-id="text-editor">\n+ <state line="390" column="21" selection-start="12695" selection-end="12695" vertical-scroll-proportion="0.59731543" />\n+ </provider>\n+ </entry>\n+ <entry file="file:///System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/fileinput.py">\n+ <provider selected="true" editor-type-id="text-editor">\n+ <state line="90" column="4" selection-start="3827" selection-end="3827" vertical-scroll-proportion="0.28391168" />\n+ </provider>\n+ </entry>\n+ <entry file="file://$PROJECT_DIR$/bs_index/wg_build.py">\n+ <provider selected="true" editor-type-id="text-editor">\n+ <state line="7" column="37" selection-start="268" selection-end="268" vertical-scroll-proportion="-0.70347005">\n+ <folding />\n+ </state>\n+ </provider>\n+ </entry>\n+ <entry file="file://$PROJECT_DIR$/bs_seeker2-build.py">\n+ <provider selected="true" editor-type-id="text-editor">\n+ <state line="15" column="102" selection-start="651" selection-end="651" vertical-scroll-proportion="0.19323671">\n+ <folding />\n+ </state>\n+ </provider>\n+ </entry>\n+ <entry file="file://$PROJECT_DIR$/bs_align/bs_single_end.py">\n+ <provider selected="true" editor-type-id="text-editor">\n+ <state line="73" column="19" selection-start="2782" selection-end="2789" vertical-scroll-proportion="0.9328859">\n+ <folding>\n+ <element signature="e#0#40#0" expanded="true" />\n+ </folding>\n+ </state>\n+ </provider>\n+ </entry>\n+ <entry file="file://$PROJECT_DIR$/bs_align/bs_rrbs.py">\n+ <provider selected="true" editor-type-id="text-editor">\n+ <state line="621" column="50" selection-start="27893" selection-end="27908" vertical-scroll-proportion="0.33221477">\n+ <folding />\n+ </state>\n+ </provider>\n+ </entry>\n+ <entry file="file://$PROJECT_DIR$/bs_align/bs_pair_end.py">\n+ <provider selected="true" editor-type-id="text-editor">\n+ <state line="734" column="76" selection-start="31798" selection-end="31798" vertical-scroll-proportion="20.067114">\n+ <folding 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file="file://$PROJECT_DIR$/README.md">\n+ <provider selected="true" editor-type-id="text-editor">\n+ <state line="77" column="25" selection-start="2888" selection-end="2895" vertical-scroll-proportion="-7.92">\n+ <folding />\n+ </state>\n+ </provider>\n+ </entry>\n+ <entry file="file://$PROJECT_DIR$/bs_utils/utils.py">\n+ <provider selected="true" editor-type-id="text-editor">\n+ <state line="14" column="0" selection-start="176" selection-end="176" vertical-scroll-proportion="0.16103059">\n+ <folding />\n+ </state>\n+ </provider>\n+ </entry>\n+ </component>\n+</project>\n+\n'

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/FilterReads.py
--- a/BSseeker2/FilterReads.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/FilterReads.py Tue Nov 05 01:55:39 2013 -0500

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python

import sys
import os
@@ -226,7 +226,7 @@
     (options, args) = parser.parse_args()

     if (options.infile is None) or (options.outfile is None) :
-        print parser.print_help()
+        parser.print_help()
         exit(-1)
     FilterReads(options.infile, options.outfile, options.keepquality)

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/README.md
--- a/BSseeker2/README.md Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/README.md Tue Nov 05 01:55:39 2013 -0500

[

b'@@ -48,9 +48,10 @@\n \n * Linux or Mac OS platform\n * One of the following Aligner\n- - [bowtie](http://bowtie-bio.sourceforge.net/)\n- - [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/) (Recommend)\n+ - [bowtie](http://bowtie-bio.sourceforge.net/) (fast)\n+ - [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/) (Default)\n - [soap](http://soap.genomics.org.cn/)\n+ - [rmap](http://www.cmb.usc.edu/people/andrewds/rmap/)\n * [Python](http://www.python.org/download/) (Version 2.6 +)\n \n (It is normally pre-installed in Linux. Type " python -V" to see the installed version.)\n@@ -74,7 +75,7 @@\n \n \t$ python FilterReads.py\n \tUsage: FilterReads.py -i <input> -o <output> [-k]\n-\tAuthor : Guo, Weilong; guoweilong@gmail.com; 2012-11-10\n+\tAuthor : Guo, Weilong; 2012-11-10\n \tUnique reads for qseq/fastq/fasta/sequencce, and filter\n \tlow quality file in qseq file.\n \n@@ -105,16 +106,16 @@\n -h, --help show this help message and exit\n -f FILE, --file=FILE Input your reference genome file (fasta)\n --aligner=ALIGNER Aligner program to perform the analysis: bowtie,\n- bowtie2, soap [Default: bowtie2]\n- -p PATH, --path=PATH Path to the aligner program. Defaults:\n- bowtie: /u/home/mcdb/weilong/install/bowtie-0.12.8\n- bowtie2:\n- /u/home/mcdb/weilong/install/bowtie2-2.0.0-beta7\n- soap: /u/home/mcdb/weilong/install/soap2.21release/\n+ bowtie2, soap, rmap [Default: bowtie]\n+ -p PATH, --path=PATH Path to the aligner program. Detected:\n+ bowtie: ~/install/bowtie\n+ bowtie2: ~/install/bowtie2\n+ rmap: ~/install/rmap_/bin\n+ soap: ~/install/soap/\n -d DBPATH, --db=DBPATH\n Path to the reference genome library (generated in\n- preprocessing genome) [Default: /u/home/mcdb/weilong/i\n- nstall/BSseeker2/bs_utils/reference_genomes]\n+ preprocessing genome) [Default: ~/install\n+ /BSseeker2/bs_utils/reference_genomes]\n -v, --version show version of BS-Seeker2\n \n Reduced Representation Bisulfite Sequencing Options:\n@@ -125,7 +126,7 @@\n certain fragments will be masked. [Default: False]\n -l LOW_BOUND, --low=LOW_BOUND\n lower bound of fragment length (excluding recognition\n- sequence such as C-CGG) [Default: 40]\n+ sequence such as C-CGG) [Default: 20]\n -u UP_BOUND, --up=UP_BOUND\n upper bound of fragment length (excluding recognition\n sequence such as C-CGG ends) [Default: 500]\n@@ -134,6 +135,7 @@\n Mael:(C-TAG), double-enzyme MspI&Mael:(C-CGG,C-TAG).\n [Default: C-CGG]\n \n+\n ##Example\n \n * Build genome index for WGBS using bowtie, path of bowtie should be included in $PATH\n@@ -150,7 +152,7 @@\n \n * Build genome index for RRBS library for double-enzyme : MspI (C-CGG) & ApeKI (G-CWGC, where W=A|T, see [IUPAC code](http://www.bioinformatics.org/sms/iupac.html))\n \n- python bs_seeker2-build.py -f genome.fa -r -c C-CGG,G-CWGC\n+ python bs_seeker2-build.py -f genome.fa -r -c C-CGG,G-CWGC --aligner=bowtie\n \n ##Tips:\n \n@@ -172,75 +174,73 @@\n ##Usage :\n \n $ python ~/install/BSseeker2/bs_seeker2-align.py -h\n- Usage: bs_seeker2-align.py [options]\n+ Usage: bs_seeker2-align.py {-i <single> | -1 <mate1> -2 <mate2>} -g <genome.fa> [options]\n \n Options:\n -h, --help show this help message and exit\n \n For single end reads:\n -i INFILE, --input=INFILE\n- Input your read file name (FORMAT: sequences,\n- '..b'_T).\n+ (7) #_of_C (methylated C, the count of reads showing C here)\n+ (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)\n \n \n - ATCGmap file\n@@ -442,7 +465,7 @@\n chr1\tT\t3009410\t--\t--\t0\t10\t0\t0\t0\t0\t0\t0\t0\t0\tna\n chr1\tC\t3009411\tCHH\tCC\t0\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0.0\n chr1\tC\t3009412\tCHG\tCC\t0\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0.0\n- chr1\tC\t3009413\tCG\tCG\t0\t10\t50\t0\t0\t0\t0\t0\t0\t0\t0.833333333333\n+ chr1\tC\t3009413\tCG\tCG\t0\t10\t50\t0\t0\t0\t0\t0\t0\t0\t0.83\n \n \n Format descriptions:\n@@ -467,14 +490,15 @@\n (14) # of reads from Crick strand mapped here, support G on Watson strand and C on Crick strand\n (15) # of reads from Crick strand mapped here, support N\n \n- (16) methylation_level = #C/(#C+#T) = (C8+C14)/(C7+C8+C11+C14); "nan" means none reads support C/T at this position.\n+ (16) methylation_level = #C/(#C+#T) = C8/(C7+C8) for Watson strand, =C14/(C11+C14) for Crick strand;\n+ "nan" means none reads support C/T at this position.\n \n \n \n Contact Information\n ============\n \n-If you still have questions on BS-Seeker 2, or you find bugs when using BS-Seeker 2, or you have suggestions, please write email to guoweilong@gmail.com (Weilong Guo).\n+If you still have questions on BS-Seeker 2, or you find bugs when using BS-Seeker 2, or you have suggestions, please write email to [Weilong Guo](guoweilong@gmail.com).\n \n \n \n@@ -556,7 +580,7 @@\n cd BSseeker2-master/\n \n \n-\xef\xbc\x884\xef\xbc\x89Run BS-Seeker2\n+(4)Run BS-Seeker2\n \n Q: Can I add the path of BS-Seeker2\'s *.py to the $PATH, so I can call\n BS-Seeker2 from anywhere?\n@@ -585,6 +609,69 @@\n bs_seeker-align.py -h\n bs_seeker-call_methylation.py -h\n \n+(5) Unique alignment\n+\n+Q: If I want to only keep alignments that map uniquely, is this an argument I should supply directly\n+to Bowtie2 (via BS Seeker 2\'s command line option), or is this an option that\'s available in\n+BS Seeker 2 itself?\n+\n+A: BS-Seeker2 reports unique alignment by default already. If you want to know how many reads\n+could have multiple hits, run BS-Seeker2 with parameter "--multiple-hit".\n+\n+\n+(6) Output\n+\n+Q: In CGmap files, why some lines shown "--" but not a motif (CG/CHG/CHH), for example:\n+\n+ chr01 C 4303711 -- CC 0.0 0 2\n+ chr01 C 4303712 -- CN 0.0 0 2\n+\n+A: In this example, the site 4303713 is "N" in genome, thus we could not decide the explict pattern.\n+\n+(7) Algorithm to remove the adapter.\n+\n+Q: What\'s the algorithm to remove the adapter\n+\n+A: BS-Seeker2 has built-in algorithm for removing the adapter, which is developed by [Weilong Guo](http://bioinfo.au.tsinghua.edu.cn/member/wguo/index.html).\n+\n+ First, if the adapter was provided as "AGATCGGAAGAGCACACGTC", only the first 10bp would be used.\n+ Second, we use semi-local alignment strategy for removing the adapters.\n+ Exmaple:\n+\n+ Read : ACCGCGTTGATCGAGTACGTACGTGGGTC\n+ Adapter : ....................ACGTGGGTCCCG\n+\n+ no_mismatch : the maximum number allowed for mismatches\n+\n+ Algorithm: (allowing 1 mismatch)\n+ -Step 1:\n+ ACCGCGTTGATCGAGTACGTACGTGGGTC\n+ ||XX\n+ ACGTGGGTCCCG\n+ -Step 2:\n+ ACCGCGTTGATCGAGTACGTACGTGGGTC\n+ X||X\n+ .ACGTGGGTCCCG\n+ -Step 3:\n+ ACCGCGTTGATCGAGTACGTACGTGGGTC\n+ XX\n+ ..ACGTGGGTCCCG\n+ -Step ...\n+ -Step N:\n+ ACCGCGTTGATCGAGTACGTACGTGGGTC\n+ |||||||||\n+ ....................ACGTGGGTCCCG\n+ Success & return!\n+\n+ Third, we also removed the synthesized bases at the end of RRBS fragments.\n+ Take the "C-CGG" cutting site as example,\n+\n+ - - C|U G G - - =>cut=> - - C =>add=> - - C|C G =>sequencing\n+ - - G G C|C - - - - G G C - - G G C\n+\n+ In our algorithm, the "CG" in "--CCG" (upper strand) was trimmed, in order to get accurate methyaltion level.\n \n \n \n+\n+\n'

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/RELEASE_NOTES
--- a/BSseeker2/RELEASE_NOTES Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/RELEASE_NOTES Tue Nov 05 01:55:39 2013 -0500

[

@@ -3,5 +3,25 @@
1. Fix bug in utils.py
2. Add UPDATE file

+v2.0.4 - July 29, 2013
+1. Update README.md (Definition of ATCGmap format)
+2. Fix the "None" output when no parameter
+3. Fix error report when using wrong path for short reads aligner
+4. MIT License
+
+V2.0.5 - Nov 31, 2013
+1. Fix bug in "bs_single_end.py" for "numbers_premapped_lst[0] += len(Unique_FW_C2T)"
+2. Make the default aligner to Bowtie
+3. Update the README file
+4. "-r N" in call-methylation will only control Wiggle file
+5. Change the output of pair-end mapping to the standard format of SAM file (the QNAME and FLAG fields)
+6. The artificially synthesized bases at the ends of RRBS fragments are removed when removing the adapters
+7. Add the total number of bases of uniquely mapped reads to the STDOUT
+8. Support "end-to-end" alignment mode in the Galaxy version
+9. Support input file in both TEXT or Compressed (.gz) format
+10. "-m" allow both INT and FLOAT as input. Ex: '-m 5' or '-m 0.05'
+11. Add mode information in output

+
+

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/.___init__.py

Binary file BSseeker2/bs_align/.___init__.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/._bs_align_utils.py

Binary file BSseeker2/bs_align/._bs_align_utils.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/._bs_pair_end.py

Binary file BSseeker2/bs_align/._bs_pair_end.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/._bs_rrbs.py

Binary file BSseeker2/bs_align/._bs_rrbs.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/._bs_single_end.py

Binary file BSseeker2/bs_align/._bs_single_end.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/._output.py

Binary file BSseeker2/bs_align/._output.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/bs_align_utils.py
--- a/BSseeker2/bs_align/bs_align_utils.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_align/bs_align_utils.py Tue Nov 05 01:55:39 2013 -0500

[

@@ -54,9 +54,15 @@

"""

-def RemoveAdapter ( read, adapter, no_mismatch ) :
+# Remove the adapter from 3' end
+def RemoveAdapter ( read, adapter, no_mismatch, rm_back=0) :
     lr = len(read)
     la = len(adapter)
+    # Check the empty adapter, namely, the reads start with the 2nd base of adapter,
+    # not including the 'A' base in front of the adapter.
+    if adapter[2:] == read[0:(la-1)] :
+        return ""
+
     for i in xrange( lr - no_mismatch ) :
         read_pos = i
         adapter_pos = 0
@@ -74,8 +80,14 @@
                     adapter_pos = adapter_pos + 1
         # while_end

+        # Cut the extra bases before the adapter
+        #     --C|CG G--  => --CNN+A+<adapter>
+        #     --G GC|C--     --GGC
         if adapter_pos == la or read_pos == lr :
-            return read[:i]
+            if i <= rm_back :
+                return ''
+            else :
+                return read[:(i-rm_back)]
     # for_end
     return read

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/bs_pair_end.py
--- a/BSseeker2/bs_align/bs_pair_end.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_align/bs_pair_end.py Tue Nov 05 01:55:39 2013 -0500

[

b'@@ -104,13 +104,13 @@\n aligner_command,\n db_path,\n tmp_path,\n- outfile, XS_pct, XS_count, show_multiple_hit=False):\n+ outfile, XS_pct, XS_count, adapter_mismatch, show_multiple_hit=False):\n \n \n #----------------------------------------------------------------\n- adapter=""\n- adapterA=""\n- adapterB=""\n+ adapter = ""\n+ adapterA = ""\n+ adapterB = ""\n if adapter_file !="":\n try :\n adapter_inf=open(adapter_file,"r")\n@@ -134,12 +134,15 @@\n logm("End 1 filename: %s"% main_read_file_1 )\n logm("End 2 filename: %s"% main_read_file_2 )\n logm("The first base (for mapping): %d"% cut1 )\n- logm("The last base (for mapping): %d"% cut2 )\n+ logm("The last base (for mapping): %d"% cut2 )\n \n- logm("-------------------------------- " )\n- logm("Un-directional library: %s" % asktag )\n logm("Path for short reads aligner: %s"% aligner_command + \'\\n\')\n logm("Reference genome library path: %s"% db_path )\n+\n+ if asktag == "Y" :\n+ logm("Un-directional library" )\n+ else :\n+ logm("Directional library")\n logm("Number of mismatches allowed: %s"% max_mismatch_no )\n \n if adapter_file !="":\n@@ -182,6 +185,9 @@\n all_trimmed=0\n all_mapped=0\n all_mapped_passed=0\n+ all_base_before_trim=0\n+ all_base_after_trim=0\n+ all_base_mapped=0\n \n all_unmapped=0\n \n@@ -192,6 +198,8 @@\n uC_lst=[0,0,0]\n \n no_my_files=0\n+ read_id_lst_1 = dict()\n+ read_id_lst_2 = dict()\n \n #----------------------------------------------------------------\n print "== Start mapping =="\n@@ -212,11 +220,14 @@\n #----------------------------------------------------------------\n outfile_1FCT = tmp_d(\'Trimmed_FCT_1.fa\'+random_id)\n outfile_1RCT = tmp_d(\'Trimmed_RCT_1.fa\'+random_id)\n- outfile_2FCT = tmp_d(\'Trimmed_FCT_2.fa\'+random_id)\n+ outfile_2RGA = tmp_d(\'Trimmed_FCT_2.fa\'+random_id)\n outfile_2RCT = tmp_d(\'Trimmed_RCT_2.fa\'+random_id)\n \n try :\n- read_inf = open(tmp_d(read_file_1),"r")\n+ if read_file_1.endswith(".gz") : # support input file ending with ".gz"\n+ read_inf = gzip.open(tmp_d(read_file_1), "rb")\n+ else :\n+ read_inf = open(tmp_d(read_file_1),"r")\n except IOError :\n print "[Error] Cannot open file : %s", tmp_d(read_file_1)\n exit(-1)\n@@ -226,128 +237,131 @@\n \n if oneline[0]=="@":\t# Illumina GAII FastQ (Lister et al Nature 2009)\n input_format="fastq"\n- n_fastq=0\n elif len(l)==1 and oneline[0]!=">": \t# pure sequences\n input_format="seq"\n elif len(l)==11:\t# Illumina GAII qseq file\n input_format="qseq"\n elif oneline[0]==">":\t# fasta\n input_format="fasta"\n- n_fasta=0\n read_inf.close()\n \n print "Detected data format: %s" % input_format\n \n #----------------------------------------------------------------\n read_file_list = [read_file_1, read_file_2]\n- outfile_FCT_list = [outfile_1FCT, outfile_2FCT]\n+ outfile_FCT_list = [outfile_1FCT, outfile_2RGA]\n outfile_RCT_list = [outfile_1RCT, outfile_2RCT]\n n_list = [0, 0]\n-\n-\n for f in range(2):\n read_file = read_file_list[f]\n outf_FCT = open(outfile_FCT_list[f], \'w\')\n- outf_RCT = open(outfile_RCT_list[f], \'w\')\n+ outf_RGA = open(outfile_RCT_list[f], \'w\')\n original_bs_reads = original_bs_reads_lst[f]\n n = n_list[f]\n-\n- seq_id = ""\n+ read_id = ""\n seq = ""\n seq_ready = "N"\n+ line_no = 0\n for line in fi'..b' :\n+ logm("Number of reads having adapter removed: %d \\n"% all_trimmed)\n+ logm("Number of bases after trimming the adapters: %d (%1.3f)" % (all_base_after_trim, float(all_base_after_trim)/all_base_before_trim) )\n \n if all_raw_reads >0:\n \n- logm("O Number of unique-hits read pairs for post-filtering: %d" % all_mapped + "\\n")\n+ logm("Number of reads rejected because of multiple hits: %d\\n" % len(Multiple_hits) )\n+ logm("Number of unique-hits reads (before post-filtering): %d" % all_mapped + "\\n")\n if asktag=="Y":\n- logm("O -- %7d FW-RC pairs mapped to Watson strand (before post-filtering)"%(numbers_premapped_lst[0]) )\n- logm("O -- %7d RC-FW pairs mapped to Watson strand (before post-filtering)"%(numbers_premapped_lst[1]) )\n- logm("O -- %7d FW-RC pairs mapped to Crick strand (before post-filtering)"%(numbers_premapped_lst[2]) )\n- logm("O -- %7d RC-FW pairs mapped to Crick strand (before post-filtering)"%(numbers_premapped_lst[3]) )\n+ logm("-- %7d FW-RC pairs mapped to Watson strand (before post-filtering)"%(numbers_premapped_lst[0]) )\n+ logm("-- %7d RC-FW pairs mapped to Watson strand (before post-filtering)"%(numbers_premapped_lst[1]) )\n+ logm("-- %7d FW-RC pairs mapped to Crick strand (before post-filtering)"%(numbers_premapped_lst[2]) )\n+ logm("-- %7d RC-FW pairs mapped to Crick strand (before post-filtering)"%(numbers_premapped_lst[3]) )\n elif asktag=="N":\n- logm("O -- %7d FW-RC pairs mapped to Watson strand (before post-filtering)"%(numbers_premapped_lst[0]) )\n- logm("O -- %7d FW-RC pairs mapped to Crick strand (before post-filtering)"%(numbers_premapped_lst[1]) )\n-\n+ logm("-- %7d FW-RC pairs mapped to Watson strand (before post-filtering)"%(numbers_premapped_lst[0]) )\n+ logm("-- %7d FW-RC pairs mapped to Crick strand (before post-filtering)"%(numbers_premapped_lst[1]) )\n+ logm("--- %d uniquely aligned pairs, where each end has mismatches <= %s"%(all_mapped_passed, max_mismatch_no) )\n+ if asktag=="Y":\n+ logm("----- %7d FW-RC pairs mapped to Watson strand"%(numbers_mapped_lst[0]) )\n+ logm("----- %7d RC-FW pairs mapped to Watson strand"%(numbers_mapped_lst[1]) )\n+ logm("----- %7d FW-RC pairs mapped to Crick strand"%(numbers_mapped_lst[2]) )\n+ logm("----- %7d RC-FW pairs mapped to Crick strand"%(numbers_mapped_lst[3]) )\n+ elif asktag=="N":\n+ logm("----- %7d FW-RC pairs mapped to Watson strand"%(numbers_mapped_lst[0]) )\n+ logm("----- %7d FW-RC pairs mapped to Crick strand"%(numbers_mapped_lst[1]) )\n \n- logm("O --- Number of reads rejected because of multiple hits: %d\\n" % len(Multiple_hits) )\n- logm("O --- %d uniquely aligned pairs, where each end has mismatches <= %s"%(all_mapped_passed, max_mismatch_no) )\n- if asktag=="Y":\n- logm("O ----- %7d FW-RC pairs mapped to Watson strand"%(numbers_mapped_lst[0]) )\n- logm("O ----- %7d RC-FW pairs mapped to Watson strand"%(numbers_mapped_lst[1]) )\n- logm("O ----- %7d FW-RC pairs mapped to Crick strand"%(numbers_mapped_lst[2]) )\n- logm("O ----- %7d RC-FW pairs mapped to Crick strand"%(numbers_mapped_lst[3]) )\n- elif asktag=="N":\n- logm("O ----- %7d FW-RC pairs mapped to Watson strand"%(numbers_mapped_lst[0]) )\n- logm("O ----- %7d FW-RC pairs mapped to Crick strand"%(numbers_mapped_lst[1]) )\n-\n- logm("O Mappability= %1.4f%%"%(100*float(all_mapped_passed)/all_raw_reads) )\n- logm("O Unmapped read pairs: %d"% all_unmapped+"\\n")\n-\n+ logm("Mappability= %1.4f%%"%(100*float(all_mapped_passed)*2/all_raw_reads) )\n+ logm("Total bases of uniquely mapped reads %7d"% all_base_mapped )\n+ logm("Unmapped read pairs: %d"% all_unmapped+"\\n")\n \n n_CG=mC_lst[0]+uC_lst[0]\n n_CHG=mC_lst[1]+uC_lst[1]\n'

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/bs_rrbs.py
--- a/BSseeker2/bs_align/bs_rrbs.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_align/bs_rrbs.py Tue Nov 05 01:55:39 2013 -0500

[

b'@@ -42,24 +42,7 @@\n # For double enzyme: cut_format="C-CGG,A-CTG"; ApekI:"G^CWGC"\n #cut_context = re.sub("-", "", cut_format)\n # Ex. cut_format="C-CGG,AT-CG,G-CWGC"\n- """\n \n- :param main_read_file:\n- :param asktag:\n- :param adapter_file:\n- :param cut_s:\n- :param cut_e:\n- :param no_small_lines:\n- :param max_mismatch_no:\n- :param aligner_command:\n- :param db_path:\n- :param tmp_path:\n- :param outfile:\n- :param XS_pct:\n- :param XS_count:\n- :param adapter_mismatch:\n- :param cut_format:\n- """\n cut_format_lst = EnumerateIUPAC(cut_format.upper().split(",")) # [\'G-CAGC\', \'AT-CG\', \'C-CGG\', \'G-CTGC\']\n cut_context = [i.replace("-","") for i in cut_format_lst] # [\'GCAGC\', \'ATCG\', \'CCGG\', \'GCTGC\']\n cut5_context = [re.match( r\'(.*)\\-(.*)\', i).group(1) for i in cut_format_lst] # [\'G\', \'AT\', \'C\', \'G\']\n@@ -106,18 +89,31 @@\n print "[Error] Cannot find adapter file : %s !" % adapter_file\n exit(-1)\n \n- logm("I Read filename: %s" % main_read_file)\n- logm("I The last cycle (for mapping): %d" % cut_e )\n- logm("I Bowtie path: %s" % aligner_command )\n- logm("I Reference genome library path: %s" % db_path )\n- logm("I Number of mismatches allowed: %s" % max_mismatch_no)\n- logm("I Adapter seq: %s" % whole_adapter_seq)\n- logm("----------------------------------------------")\n+ logm("Read filename: %s" % main_read_file)\n+ logm("The first base (for mapping): %d"% cut_s )\n+ logm("The last base (for mapping): %d"% cut_e )\n+\n+ logm("Path for short reads aligner: %s"% aligner_command + \'\\n\')\n+ logm("Reference genome library path: %s"% db_path )\n+\n+ if asktag == "Y" :\n+ logm("Un-directional library" )\n+ else :\n+ logm("Directional library")\n+\n+ logm("Number of mismatches allowed: %s"% max_mismatch_no )\n+\n+ if adapter_file !="":\n+ logm("Adapter seq: %s" % whole_adapter_seq)\n+ logm("-------------------------------- " )\n \n #----------------------------------------------------------------\n all_raw_reads=0\n all_tagged=0\n all_tagged_trimmed=0\n+ all_base_before_trim=0\n+ all_base_after_trim=0\n+ all_base_mapped=0\n all_mapped=0\n all_mapped_passed=0\n n_cut_tag_lst={}\n@@ -135,6 +131,9 @@\n num_mapped_FW_G2A = 0\n num_mapped_RC_G2A = 0\n \n+ # Count of nucleotides, which should be cut before the adapters\n+ Extra_base_cut_5end_adapter = max([ abs(len(i)-len(j)) for i,j in zip(cut5_context, cut3_context)])\n+\n #===============================================\n # directional sequencing\n #===============================================\n@@ -156,72 +155,71 @@\n \n #--- Checking input format ------------------------------------------\n try :\n- read_inf=open(read_file,"r")\n+ if read_file.endswith(".gz") : # support input file ending with ".gz"\n+ read_inf = gzip.open(read_file, "rb")\n+ else :\n+ read_inf=open(read_file,"r")\n except IOError:\n print "[Error] Cannot open input file : %s" % read_file\n exit(-1)\n \n- oneline=read_inf.readline()\n- l=oneline.split()\n- n_fastq=0\n- n_fasta=0\n- input_format=""\n- if oneline[0]=="@":\t# FastQ\n- input_format="fastq"\n- elif len(l)==1 and oneline[0]!=">": # pure sequences\n- input_format="seq"\n- elif len(l)==11: # Illumina qseq\n- input_format="qseq"\n- elif oneline[0]==">": # fasta\n- input_format="fasta"\n+ oneline = read_inf.readline()\n+ l = oneline.split()\n+ input_format = ""\n+ if oneline[0]=="@":\n+ input_format = "fastq"\n+ elif len(l)==1 and oneline[0]!=">" :\n+ input_format = "seq"\n+ elif len(l)==11:\n+ input_format'..b'read_file, no_my_files))\n print "--> %s (%d) "%(read_file, no_my_files)\n del original_bs_reads\n delete_files(WC2T, CC2T, WG2A, CG2A)\n-\n-\n-\n # End of un-directional library\n \n delete_files(tmp_path)\n \n \n- logm("O Number of raw reads: %d "% all_raw_reads)\n- if all_raw_reads >0:\n- logm("O Number of CGG/TGG tagged reads: %d (%1.3f)"%(all_tagged,float(all_tagged)/all_raw_reads))\n+ logm("Number of raw reads: %d "% all_raw_reads)\n+ if all_raw_reads>0:\n+ logm("Number of raw reads with CGG/TGG at 5\' end: %d (%1.3f)"%(all_tagged,float(all_tagged)/all_raw_reads))\n for kk in range(len(n_cut_tag_lst)):\n- logm("O Number of raw reads with %s tag: %d (%1.3f)"%(cut3_tag_lst[kk],n_cut_tag_lst[cut3_tag_lst[kk]],float(n_cut_tag_lst[cut3_tag_lst[kk]])/all_raw_reads))\n- logm("O Number of CGG/TGG reads having adapter removed: %d "%all_tagged_trimmed)\n- logm("O Number of reads rejected because of multiple hits: %d\\n" % len(Multiple_hits) )\n- logm("O Number of unique-hits reads for post-filtering: %d"%all_mapped)\n+ logm("Number of raw reads with tag %s: %d (%1.3f)"%(cut3_tag_lst[kk],n_cut_tag_lst[cut3_tag_lst[kk]],float(n_cut_tag_lst[cut3_tag_lst[kk]])/all_raw_reads))\n+ if adapter_seq!="" :\n+ logm("Number of reads having adapter removed: %d "%all_tagged_trimmed)\n+ logm("Number of bases in total: %d "%all_base_before_trim)\n+ if adapter_seq!="" :\n+ logm("Number of bases after trimming the adapters: %d (%1.3f)"%(all_base_after_trim, float(all_base_after_trim)/all_base_before_trim ) )\n+ logm("Number of reads are rejected because of multiple hits: %d\\n" % len(Multiple_hits) )\n+ logm("Number of unique-hits reads (before post-filtering): %d"%all_mapped)\n \n- logm("O ------ %d uniquely aligned reads, passed fragment check, with mismatches <= %s"%(all_mapped_passed, max_mismatch_no))\n- logm("O Mappability= %1.4f%%"%(100*float(all_mapped_passed)/all_raw_reads))\n+ logm("------ %d uniquely aligned reads, passed fragment check, with mismatches <= %s"%(all_mapped_passed, max_mismatch_no))\n+ logm("Mappability= %1.4f%%"%(100*float(all_mapped_passed)/all_raw_reads))\n+ logm("Total bases of uniquely mapped reads %7d"% all_base_mapped )\n \n- if asktag=="Y": # undiretional\n+ if asktag=="Y": # un-diretional\n logm(" ---- %7d FW reads mapped to Watson strand"%(num_mapped_FW_C2T) )\n logm(" ---- %7d RC reads mapped to Watson strand"%(num_mapped_FW_G2A) )\n logm(" ---- %7d FW reads mapped to Crick strand"%(num_mapped_RC_C2T) )\n@@ -1021,16 +1038,17 @@\n elif asktag=="N": # directional\n logm(" ---- %7d FW reads mapped to Watson strand"%(num_mapped_FW_C2T) )\n logm(" ---- %7d FW reads mapped to Crick strand"%(num_mapped_RC_C2T) )\n+ logm("Total bases of uniquely mapped reads %7d"% all_base_mapped )\n \n- n_CG=mC_lst[0]+uC_lst[0]\n- n_CHG=mC_lst[1]+uC_lst[1]\n- n_CHH=mC_lst[2]+uC_lst[2]\n+ n_CG = mC_lst[0] + uC_lst[0]\n+ n_CHG = mC_lst[1] + uC_lst[1]\n+ n_CHH = mC_lst[2] + uC_lst[2]\n \n logm("----------------------------------------------")\n- logm("M Methylated C in mapped reads ")\n- logm("M mCG %1.3f%%"%((100*float(mC_lst[0])/n_CG) if n_CG != 0 else 0))\n- logm("M mCHG %1.3f%%"%((100*float(mC_lst[1])/n_CHG) if n_CHG != 0 else 0))\n- logm("M mCHH %1.3f%%"%((100*float(mC_lst[2])/n_CHH) if n_CHH != 0 else 0))\n+ logm("Methylated C in mapped reads ")\n+ logm(" mCG %1.3f%%"%( (100 * float(mC_lst[0]) / n_CG) if n_CG!=0 else 0))\n+ logm(" mCHG %1.3f%%"%( (100 * float(mC_lst[1]) / n_CHG) if n_CHG!=0 else 0))\n+ logm(" mCHH %1.3f%%"%( (100 * float(mC_lst[2]) / n_CHH) if n_CHH!=0 else 0))\n logm("----------------------------------------------")\n logm("------------------- END ----------------------")\n \n'

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/bs_single_end.py
--- a/BSseeker2/bs_align/bs_single_end.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_align/bs_single_end.py Tue Nov 05 01:55:39 2013 -0500

[

b'@@ -1,6 +1,7 @@\n import fileinput, os, time, random, math\n from bs_utils.utils import *\n from bs_align_utils import *\n+import gzip\n \n #----------------------------------------------------------------\n # Read from the mapped results, return lists of unique / multiple-hit reads\n@@ -77,20 +78,23 @@\n \n \n #----------------------------------------------------------------\n- logm("Read filename: %s"% main_read_file )\n- logm("Un-directional library: %s" % asktag )\n- logm("The first base (for mapping): %d" % cut1)\n- logm("The last base (for mapping): %d" % cut2)\n- logm("Max. lines per mapping: %d"% no_small_lines)\n- logm("Aligner: %s" % aligner_command)\n- logm("Reference genome library path: %s" % db_path )\n- logm("Number of mismatches allowed: %s" % max_mismatch_no )\n+ logm("Read filename: %s" % main_read_file)\n+ logm("The first base (for mapping): %d"% cut1 )\n+ logm("The last base (for mapping): %d"% cut2 )\n+\n+ logm("Path for short reads aligner: %s"% aligner_command + \'\\n\')\n+ logm("Reference genome library path: %s"% db_path )\n+\n+ if asktag == "Y" :\n+ logm("Un-directional library" )\n+ else :\n+ logm("Directional library")\n+\n+ logm("Number of mismatches allowed: %s"% max_mismatch_no )\n+\n if adapter_file !="":\n- if asktag=="N":\n- logm("Adapter to be removed from 3\' reads: %s"%(adapter.rstrip("\\n")))\n- elif asktag=="Y":\n- logm("Adapter to be removed from 3\' FW reads: %s"%(adapter_fw.rstrip("\\n")) )\n- logm("Adapter to be removed from 3\' RC reads: %s"%(adapter_rc.rstrip("\\n")) )\n+ logm("Adapter seq: %s" % adapter_fw)\n+ logm("-------------------------------- " )\n #----------------------------------------------------------------\n \n # helper method to join fname with tmp_path\n@@ -109,9 +113,12 @@\n \n #---- Stats ------------------------------------------------------------\n all_raw_reads=0\n- all_trimed=0\n+ all_trimmed=0\n all_mapped=0\n all_mapped_passed=0\n+ all_base_before_trim=0\n+ all_base_after_trim=0\n+ all_base_mapped=0\n \n numbers_premapped_lst=[0,0,0,0]\n numbers_mapped_lst=[0,0,0,0]\n@@ -119,7 +126,6 @@\n mC_lst=[0,0,0]\n uC_lst=[0,0,0]\n \n-\n no_my_files=0\n \n #----------------------------------------------------------------\n@@ -132,7 +138,7 @@\n random_id = ".tmp-"+str(random.randint(1000000,9999999))\n \n #-------------------------------------------------------------------\n- # undirectional sequencing\n+ # un-directional sequencing\n #-------------------------------------------------------------------\n if asktag=="Y": \n \n@@ -146,74 +152,70 @@\n #----------------------------------------------------------------\n # detect format of input file\n try :\n- read_inf=open(read_file,"r")\n+ if read_file.endswith(".gz") : # support input file ending with ".gz"\n+ read_inf = gzip.open(read_file, "rb")\n+ else :\n+ read_inf=open(read_file,"r")\n except IOError :\n print "[Error] Cannot open input file : %s" % read_file\n exit(-1)\n \n- oneline=read_inf.readline()\n- l=oneline.split()\n- input_format=""\n- if oneline[0]=="@":\t# fastq\n- input_format="fastq"\n- n_fastq=0\n- elif len(l)==1 and oneline[0]!=">": # pure sequences\n- input_format="seq"\n- elif len(l)==11: # qseq\n- input_format="qseq"\n- elif oneline[0]==">":\t# fasta\n- input_format="fasta"\n- n_fasta=0\n+ oneline = read_inf.readline()\n+ l = oneline.split()\n+ input_format = ""\n+ if oneline[0]=="@":\n+ input_format = "fastq"\n+ elif len(l)==1 and oneline[0]!=">":\n+ input_format = "se'..b't2-cut1+1)\n \n@@ -612,7 +614,6 @@\n outf_MH.close()\n \n \n-\n FW_C2T_uniq_lst=[[FW_C2T_U[u][1],u] for u in Unique_FW_C2T]\n RC_C2T_uniq_lst=[[RC_C2T_U[u][1],u] for u in Unique_RC_C2T]\n FW_C2T_uniq_lst.sort()\n@@ -633,7 +634,6 @@\n chr_length = dict()\n for ali_unique_lst, ali_dic in [(FW_C2T_uniq_lst,FW_C2T_U),(RC_C2T_uniq_lst,RC_C2T_U)]:\n nn += 1\n- mapped_chr0 = ""\n for header in ali_unique_lst:\n _, mapped_chr, mapped_location, cigar = ali_dic[header]\n original_BS = original_bs_reads[header]\n@@ -641,11 +641,6 @@\n if mapped_chr not in gseq :\n gseq[mapped_chr] = deserialize(db_d(mapped_chr))\n chr_length[mapped_chr] = len(gseq[mapped_chr])\n- #if mapped_chr != mapped_chr0:\n- # my_gseq = deserialize(db_d(mapped_chr))\n- # chr_length = len(my_gseq)\n- # mapped_chr0 = mapped_chr\n- #-------------------------------------\n \n r_start, r_end, g_len = get_read_start_end_and_genome_length(cigar)\n \n@@ -664,7 +659,8 @@\n \n if len(r_aln) == len(g_aln):\n N_mismatch = N_MIS(r_aln, g_aln) #+ original_BS_length - (r_end - r_start) # mismatches in the alignment + soft clipped nucleotides\n- if N_mismatch <= int(max_mismatch_no):\n+ mm_no=float(max_mismatch_no)\n+ if (mm_no>=1 and N_mismatch<=mm_no) or (mm_no<1 and N_mismatch<=(mm_no*len(r_aln)) ):\n numbers_mapped_lst[nn-1] += 1\n all_mapped_passed += 1\n methy = methy_seq(r_aln, g_aln+next)\n@@ -678,6 +674,7 @@\n XS = 1\n \n outfile.store(header, N_mismatch, FR, mapped_chr, mapped_strand, mapped_location, cigar, original_BS, methy, XS, output_genome = output_genome)\n+ all_base_mapped += len(original_BS)\n \n #----------------------------------------------------------------\n logm("--> %s (%d) "%(read_file,no_my_files))\n@@ -686,14 +683,16 @@\n \n #----------------------------------------------------------------\n \n-# outf.close()\n delete_files(tmp_path)\n \n logm("Number of raw reads: %d \\n"% all_raw_reads)\n if all_raw_reads >0:\n- logm("Number of reads having adapter removed: %d \\n" % all_trimed )\n- logm("Number of reads rejected because of multiple hits: %d\\n" % len(Multiple_hits) )\n- logm("Number of unique-hits reads for post-filtering: %d\\n" % all_mapped)\n+ logm("Number of bases in total: %d "%all_base_before_trim)\n+ if adapter != "" :\n+ logm("Number of reads having adapter removed: %d \\n" % all_trimmed )\n+ logm("Number of bases after trimming the adapters: %d (%1.3f)"%(all_base_after_trim, float(all_base_after_trim)/all_base_before_trim) )\n+ logm("Number of reads are rejected because of multiple hits: %d\\n" % len(Multiple_hits) )\n+ logm("Number of unique-hits reads (before post-filtering): %d\\n" % all_mapped)\n if asktag=="Y":\n logm(" ---- %7d FW reads mapped to Watson strand (before post-filtering)"%(numbers_premapped_lst[0]) )\n logm(" ---- %7d RC reads mapped to Watson strand (before post-filtering)"%(numbers_premapped_lst[1]) )\n@@ -713,6 +712,8 @@\n logm(" ---- %7d FW reads mapped to Watson strand"%(numbers_mapped_lst[0]) )\n logm(" ---- %7d FW reads mapped to Crick strand"%(numbers_mapped_lst[1]) )\n logm("Mappability= %1.4f%%"%(100*float(all_mapped_passed)/all_raw_reads) )\n+ logm("Total bases of uniquely mapped reads %7d"% all_base_mapped )\n+\n \n n_CG=mC_lst[0]+uC_lst[0]\n n_CHG=mC_lst[1]+uC_lst[1]\n'

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_align/output.py
--- a/BSseeker2/bs_align/output.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_align/output.py Tue Nov 05 01:55:39 2013 -0500

[

@@ -81,3 +81,53 @@
                           ('XG', output_genome))

             self.f.write(a)
+
+
+    def store2(self, qname, flag, N_mismatch, FR, refname, strand, pos, cigar, original_BS, methy, STEVE, rnext = -1, pnext = -1, qual = None, output_genome = None,
+              rrbs = False, my_region_serial = -1, my_region_start = 0, my_region_end = 0):
+
+        if self.format == BS_SEEKER1:
+
+            # remove the soft clipped bases from the read
+            # this is done for backwards compatibility with the old format
+            r_start, r_end, _ = get_read_start_end_and_genome_length(cigar)
+            original_BS = original_BS[r_start : r_end]
+
+            if rrbs:
+                self.f.write('%s\t%2d\t%s\t%s%s%s\t%s\t%s\t%s\t%d\n' % (qname, N_mismatch, FR, refname, strand, str(pos+1).zfill(10), output_genome, original_BS, methy, STEVE))
+            else:
+                self.f.write('%s\t%2d\t%s\t%s%s%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\n' % (qname, N_mismatch, FR, refname, strand, str(pos+1).zfill(10), output_genome, original_BS, methy, my_region_serial, my_region_start, my_region_end, STEVE))
+
+
+        elif self.format == BAM or self.format == SAM:
+
+            a = pysam.AlignedRead()
+            a.qname = qname
+            a.seq = original_BS if strand == '+' else reverse_compl_seq(original_BS)
+            a.flag = flag
+            a.tid = self.chrom_ids[refname]
+            a.pos = pos
+            a.mapq = 255
+            a.cigar = cigar if strand == '+' else list(reversed(cigar))
+            a.rnext = rnext if rnext == -1 else self.chrom_ids[rnext]
+            a.pnext = pnext
+            a.qual= qual
+            if rrbs:
+                a.tags = (('XO', FR),
+                          ('XS', STEVE),
+                          ('NM', N_mismatch),
+                          ('XM', methy),
+                          ('XG', output_genome),
+                          ('YR', my_region_serial),
+                          ('YS', my_region_start),
+                          ('YE', my_region_end)
+                          )
+
+            else:
+                a.tags = (('XO', FR),
+                          ('XS', STEVE),
+                          ('NM', N_mismatch),
+                          ('XM', methy),
+                          ('XG', output_genome))
+
+            self.f.write(a)

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_index/.___init__.py

Binary file BSseeker2/bs_index/.___init__.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_index/._rrbs_build.py

Binary file BSseeker2/bs_index/._rrbs_build.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_index/._wg_build.py

Binary file BSseeker2/bs_index/._wg_build.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_index/wg_build.py
--- a/BSseeker2/bs_index/wg_build.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_index/wg_build.py Tue Nov 05 01:55:39 2013 -0500

[

@@ -3,8 +3,8 @@

def wg_build(fasta_file, build_command, ref_path, aligner):

-    # ref_path is a string that containts the directory where the reference genomes are stored with
-    # the input fasta filename appended
+    # ref_path is a string that contains the directory where the reference genomes are stored with
+    # the input Fasta filename appended
     ref_path = os.path.join(ref_path,
                             os.path.split(fasta_file)[1] + '_'+aligner)

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_seeker2-align.py
--- a/BSseeker2/bs_seeker2-align.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_seeker2-align.py Tue Nov 05 01:55:39 2013 -0500

[

b'@@ -1,4 +1,4 @@\n-#!/usr/bin/python\n+#!/usr/bin/env python\n \n from optparse import OptionParser, OptionGroup\n import re\n@@ -7,44 +7,47 @@\n from bs_align.bs_pair_end import *\n from bs_align.bs_single_end import *\n from bs_align.bs_rrbs import *\n-from bs_utils.utils import *\n+#import re\n+#from bs_utils.utils import *\n \n \n if __name__ == \'__main__\':\n \n- parser = OptionParser()\n+ parser = OptionParser(usage="Usage: %prog {-i <single> | -1 <mate1> -2 <mate2>} -g <genome.fa> [options]")\n # option group 1\n opt_group = OptionGroup(parser, "For single end reads")\n- opt_group.add_option("-i", "--input", type="string", dest="infilename",help="Input your read file name (FORMAT: sequences, fastq, qseq,fasta)", metavar="INFILE")\n+ opt_group.add_option("-i", "--input", type="string", dest="infilename",help="Input read file (FORMAT: sequences, qseq, fasta, fastq). Ex: read.fa or read.fa.gz", metavar="INFILE")\n parser.add_option_group(opt_group)\n \n # option group 2\n opt_group = OptionGroup(parser, "For pair end reads")\n- opt_group.add_option("-1", "--input_1", type="string", dest="infilename_1",help="Input your read file end 1 (FORMAT: sequences, qseq, fasta, fastq)", metavar="FILE")\n- opt_group.add_option("-2", "--input_2", type="string", dest="infilename_2",help="Input your read file end 2 (FORMAT: sequences, qseq, fasta, fastq)", metavar="FILE")\n- opt_group.add_option("--minins",type = "int",dest = "min_insert_size", help="The minimum insert size for valid paired-end alignments [Default: %default]", default = -1)\n- opt_group.add_option("--maxins",type = "int",dest = "max_insert_size", help="The maximum insert size for valid paired-end alignments [Default: %default]", default = 400)\n+ opt_group.add_option("-1", "--input_1", type="string", dest="infilename_1",help="Input read file, mate 1 (FORMAT: sequences, qseq, fasta, fastq)", metavar="FILE")\n+ opt_group.add_option("-2", "--input_2", type="string", dest="infilename_2",help="Input read file, mate 2 (FORMAT: sequences, qseq, fasta, fastq)", metavar="FILE")\n+ opt_group.add_option("-I", "--minins",type = "int",dest = "min_insert_size", help="The minimum insert size for valid paired-end alignments [Default: %default]", default = 0)\n+ opt_group.add_option("-X", "--maxins",type = "int",dest = "max_insert_size", help="The maximum insert size for valid paired-end alignments [Default: %default]", default = 500)\n parser.add_option_group(opt_group)\n \n # option group 3\n opt_group = OptionGroup(parser, "Reduced Representation Bisulfite Sequencing Options")\n- opt_group.add_option("-r", "--rrbs", action="store_true", dest="rrbs", default = False, help = \'Process reads from Reduced Representation Bisulfite Sequencing experiments\')\n+ opt_group.add_option("-r", "--rrbs", action="store_true", dest="rrbs", default = False, help = \'Map reads to the Reduced Representation genome\')\n opt_group.add_option("-c", "--cut-site", type="string",dest="cut_format", help="Cutting sites of restriction enzyme. Ex: MspI(C-CGG), Mael:(C-TAG), double-enzyme MspI&Mael:(C-CGG,C-TAG). [Default: %default]", metavar="pattern", default = "C-CGG")\n- opt_group.add_option("-L", "--low", type = "int", dest="rrbs_low_bound", help="lower bound of fragment length (excluding C-CGG ends) [Default: %default]", default = 40)\n- opt_group.add_option("-U", "--up", type = "int", dest="rrbs_up_bound", help="upper bound of fragment length (excluding C-CGG ends) [Default: %default]", default = 500)\n+ opt_group.add_option("-L", "--low", type = "int", dest="rrbs_low_bound", help="Lower bound of fragment length (excluding C-CGG ends) [Default: %default]", default = 20)\n+ opt_group.add_option("-U", "--up", type = "int", dest="rrbs_up_bound", help="Upper bound of fragment length (excluding C-CGG ends) [Default: %default]", default = 500)\n parser.add_option_group(opt_group)\n \n # option group 4\n opt_group = OptionGroup(parser, "General options")\n opt_grou'..b'+ logm("Mode: Bowtie2, local alignment")\n+ else :\n+ logm("Mode: Bowtie2, end-to-end alignment")\n+\n+\n tmp_path = tempfile.mkdtemp(prefix=\'bs_seeker2_%s_-%s-TMP-\' % (os.path.split(outfilename)[1], aligner_title ), dir = options.temp_dir)\n \n \n (XS_x, XS_y) = options.XS_filter.split(",")\n XS_pct = float(XS_x)\n XS_count = int(XS_y)\n- logm(\'Filter for tag XS: #(mCH)/#(all CH)>%f and #(mCH)>%d\' % (XS_pct, XS_count))\n+ logm(\'Filter for tag XS: #(mCH)/#(all CH)>%.2f%% and #(mCH)>%d\' % (XS_pct*100, XS_count))\n \n \n logm(\'Temporary directory: %s\' % tmp_path)\n@@ -253,8 +293,8 @@\n logm(\'Single end\')\n \n aligner_command = aligner_exec + aligner_options_string() + \\\n- { BOWTIE : \' %(reference_genome)s -f %(input_file)s %(output_file)s\',\n- BOWTIE2 : \' -x %(reference_genome)s -f -U %(input_file)s -S %(output_file)s\',\n+ { BOWTIE : \' -k 2 %(reference_genome)s -f %(input_file)s %(output_file)s\',\n+ BOWTIE2 : \' -k 2 -x %(reference_genome)s -f -U %(input_file)s -S %(output_file)s\',\n SOAP : \' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file)s\',\n RMAP : \' -c %(reference_genome)s.fa -o %(output_file)s %(input_file)s\'\n }[options.aligner]\n@@ -263,7 +303,6 @@\n if options.rrbs: # RRBS scan\n bs_rrbs(options.infilename,\n asktag,\n- # options.rrbs_taginfo,\n options.adapter_file,\n options.cutnumber1,\n options.cutnumber2,\n@@ -299,18 +338,18 @@\n else:\n logm(\'Pair end\')\n # pair end specific default options\n- aligner_options = dict({BOWTIE: {\'--ff\' : asktag == \'N\',\n- \'--fr\' : asktag == \'Y\',\n+ aligner_options = dict({BOWTIE: {\'--fr\' : True,\n \'-X\' : options.max_insert_size,\n- \'-I\' : options.min_insert_size if options.min_insert_size > 0 else None\n+ \'-I\' : options.min_insert_size if options.min_insert_size > 0 else None,\n+ \'-a\' : True # "-k 2" in bowtie would not report the best two\n },\n BOWTIE2 : {\n- \'--ff\' : asktag == \'N\',\n- \'--fr\' : asktag == \'Y\',\n+ \'--fr\' : True,\n \'-X\' : options.max_insert_size,\n \'-I\' : options.min_insert_size if options.min_insert_size > 0 else None,\n \'--no-discordant\' : True,\n- \'--no-mixed\' : True\n+ \'--no-mixed\' : True,\n+ \'-k\' : 2\n },\n SOAP: {\n \'-x\' : options.max_insert_size,\n@@ -328,6 +367,11 @@\n \n logm(\'Aligner command: %s\' % aligner_command)\n \n+ if \'--end-to-end\' not in aligner_options:\n+ aligner_options_defaults[BOWTIE2].update({\'-D\' : 50})\n+ else:\n+ aligner_options_defaults[BOWTIE2].update({\'-D\' : 50, \'-L\': 15, \'--score-min\': \'L,-0.6,-0.6\' })\n+\n bs_pair_end(options.infilename_1,\n options.infilename_2,\n asktag,\n@@ -342,6 +386,7 @@\n outfile,\n XS_pct,\n XS_count,\n+ options.adapter_mismatch,\n options.Output_multiple_hit\n )\n \n'

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_seeker2-build.py
--- a/BSseeker2/bs_seeker2-build.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_seeker2-build.py Tue Nov 05 01:55:39 2013 -0500

[

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python

import os
from optparse import OptionParser, OptionGroup
@@ -12,8 +12,8 @@
     parser = OptionParser()

     parser.add_option("-f", "--file", dest="filename", help="Input your reference genome file (fasta)", metavar="FILE")
-    parser.add_option("--aligner", dest="aligner", help="Aligner program to perform the analysis: " + ', '.join(supported_aligners) + " [Default: %default]", metavar="ALIGNER", default = BOWTIE2)
-    parser.add_option("-p", "--path", dest="aligner_path", help="Path to the aligner program. Defaults: " +' '*70+ '\t'.join(('%s: %s '+' '*70) % (al, aligner_path[al]) for al in sorted(supported_aligners)),
+    parser.add_option("--aligner", dest="aligner", help="Aligner program to perform the analysis: " + ', '.join(supported_aligners) + " [Default: %default]", metavar="ALIGNER", default = BOWTIE)
+    parser.add_option("-p", "--path", dest="aligner_path", help="Path to the aligner program. Detected: " +' '*70+ '\t'.join(('%s: %s '+' '*70) % (al, aligner_path[al]) for al in sorted(supported_aligners)),
                   metavar="PATH")
     parser.add_option("-d", "--db", type="string", dest="dbpath", help="Path to the reference genome library (generated in preprocessing genome) [Default: %default]", metavar="DBPATH", default = reference_genome_path)

@@ -23,7 +23,7 @@
     rrbs_opts = OptionGroup(parser, "Reduced Representation Bisulfite Sequencing Options",
                                 "Use this options with conjuction of -r [--rrbs]")
     rrbs_opts.add_option("-r", "--rrbs", action="store_true", dest="rrbs", help = 'Build index specially for Reduced Representation Bisulfite Sequencing experiments. Genome other than certain fragments will be masked. [Default: %default]', default = False)
-    rrbs_opts.add_option("-l", "--low",type= "int", dest="low_bound", help="lower bound of fragment length (excluding recognition sequence such as C-CGG) [Default: %default]", default = 40)
+    rrbs_opts.add_option("-l", "--low",type= "int", dest="low_bound", help="lower bound of fragment length (excluding recognition sequence such as C-CGG) [Default: %default]", default = 20)
     rrbs_opts.add_option("-u", "--up", type= "int", dest="up_bound", help="upper bound of fragment length (excluding recognition sequence such as C-CGG ends) [Default: %default]", default = 500)
     rrbs_opts.add_option("-c", "--cut-site", type= "string", dest="cut_format", help="Cut sites of restriction enzyme. Ex: MspI(C-CGG), Mael:(C-TAG), double-enzyme MspI&Mael:(C-CGG,C-TAG). [Default: %default]", default = "C-CGG")
     parser.add_option_group(rrbs_opts)
@@ -33,7 +33,7 @@

     # if no options were given by the user, print help and exit
     if len(sys.argv) == 1:
-        print parser.print_help()
+        parser.print_help()
         exit(0)

     if options.version :
@@ -44,7 +44,11 @@

     rrbs = options.rrbs

-    fasta_file=os.path.expanduser(options.filename)
+    if options.filename is not None :
+        fasta_file=os.path.expanduser(options.filename)
+    else :
+        error("Please specify the genome file (Fasta) using \"-f\"")
+
     if fasta_file is None:
         error('Fasta file for the reference genome must be supported')

@@ -69,9 +73,14 @@

     print "Reference genome file: %s" % fasta_file
     print "Reduced Representation Bisulfite Sequencing: %s" % rrbs
+    print "Short reads aligner you are using: %s" % options.aligner
     print "Builder path: %s" % builder_exec
+
     #---------------------------------------------------------------

+    if not os.path.isfile( builder_exec ) :
+        error("Cannot file program %s for execution." % builder_exec)
+
     ref_path = options.dbpath

     if os.path.exists(ref_path):

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_seeker2-call_methylation.py
--- a/BSseeker2/bs_seeker2-call_methylation.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_seeker2-call_methylation.py Tue Nov 05 01:55:39 2013 -0500

[

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python

from optparse import OptionParser, OptionGroup
from bs_utils.utils import *
@@ -71,7 +71,7 @@

     # if no options were given by the user, print help and exit
     if len(sys.argv) == 1:
-        print parser.print_help()
+        parser.print_help()
         exit(0)

     if options.version :
@@ -133,8 +133,6 @@
         nuc, context, subcontext = context_calling(chrom_seq, col.pos)
         total_reads = 0

-
-
         for pr in col.pileups:
         #     print pr
              if (not pr.indel) : # skip indels
@@ -152,7 +150,6 @@
                     print 'WARNING: read %s has an invalid alignment. Discarding.. ' % pr.alignment.qname
                     continue
                 read_nuc = pr.alignment.seq[pr.qpos]
-         #       print "read_nuc=", read_nuc
                 if pr.alignment.is_reverse:
                     ATCG_rev[read_nuc] += 1
                 else:
@@ -194,7 +191,8 @@
                 wiggle.write('%d\t%f\n' % (pos, meth_level))
             else :
                 wiggle.write('%d\t-%f\n' % (pos, meth_level))
-            CGmap.write('%(chrom)s\t%(nuc)s\t%(pos)d\t%(context)s\t%(subcontext)s\t%(meth_level_string)s\t%(meth_cytosines)s\t%(all_cytosines)s\n' % locals())
+
+        CGmap.write('%(chrom)s\t%(nuc)s\t%(pos)d\t%(context)s\t%(subcontext)s\t%(meth_level_string)s\t%(meth_cytosines)s\t%(all_cytosines)s\n' % locals())
     ATCGmap.close()
     CGmap.close()
     wiggle.close()

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_utils/.___init__.py

Binary file BSseeker2/bs_utils/.___init__.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_utils/._utils.py

Binary file BSseeker2/bs_utils/._utils.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/bs_utils/utils.py
--- a/BSseeker2/bs_utils/utils.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/bs_utils/utils.py Tue Nov 05 01:55:39 2013 -0500

[

@@ -23,7 +23,7 @@

def show_version() :
     print ""
-    print "     BS-Seeker2 v2.0.3 - May 19, 2013     "
+    print "     BS-Seeker2 v2.0.5 - Nov 5, 2013     "
     print ""

@@ -135,14 +135,15 @@
                              SOAP    : '--soap-',
                              RMAP    : '--rmap-' }

-aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or default_path))
-                    for aligner, default_path in
-                           [(BOWTIE,'~/bowtie-0.12.7/'),
-                            (BOWTIE2, '~/bowtie-0.12.7/'),
-                            (SOAP, '~/soap2.21release/'),
-                            (RMAP, '~/rmap_v2.05/bin')
-                            ])
-
+#aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or default_path))
+#                    for aligner, default_path in
+#                           [(BOWTIE,'~/bowtie/'),
+#                            (BOWTIE2, '~/bowtie2/'),
+#                            (SOAP, '~/soap/'),
+#                            (RMAP, '~/rmap/bin')
+#                            ])
+aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or "None"))
+                    for aligner in [(BOWTIE), (BOWTIE2), (SOAP), (RMAP)])

reference_genome_path = os.path.join(os.path.split(globals()['__file__'])[0],'reference_genomes')

@@ -214,7 +215,10 @@
     """ Splits a file (equivalend to UNIX split -l ) """
     fno = 0
     lno = 0
-    INPUT = open(filename, 'r')
+    if filename.endswith(".gz") :
+        INPUT = gzip.open(filename, 'rb')
+    else :
+        INPUT = open(filename, 'r')
     output = None
     for l in INPUT:
         if lno == 0:
@@ -321,7 +325,10 @@

     commands = [(cmd[0], open(cmd[1], 'w')) if type(cmd) is tuple else (cmd, None) for cmd in commands]

-    logm('Starting commands:\n' + '\n'.join([cmd for cmd, stdout in commands]))
+    #logm('Starting commands:\n' + '\n'.join([cmd for cmd, stdout in commands]))
+    logm('Starting commands:')
+    for cmd, stdout in commands :
+        logm("Launched: "+cmd)
     for i, proc in enumerate([subprocess.Popen(args = shlex.split(cmd), stdout = stdout) for cmd, stdout in commands]):
         return_code = proc.wait()
         logm('Finished: ' + commands[i][0])

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/galaxy/.___init__.py

Binary file BSseeker2/galaxy/.___init__.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/galaxy/._bs_seeker2_wrapper.py

Binary file BSseeker2/galaxy/._bs_seeker2_wrapper.py has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/galaxy/._bs_seeker2_wrapper.xml

Binary file BSseeker2/galaxy/._bs_seeker2_wrapper.xml has changed

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/galaxy/bs_seeker2_wrapper.py
--- a/BSseeker2/galaxy/bs_seeker2_wrapper.py Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/galaxy/bs_seeker2_wrapper.py Tue Nov 05 01:55:39 2013 -0500

[

@@ -114,7 +114,6 @@
                                     ('_rrbs_%s_%s' % (getopt(args[ALIGN], '-l', '--low', '40'),
                                                       getopt(args[ALIGN], '-u', '--up', '500'))
                                      if len(set(['-r', '--rrbs']) & set(args[ALIGN])) > 0 else '') +
-
                                     '_' + args[ALIGN]['--aligner'])
                                     })
     run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-call_methylation.py'), args[CALL_METHYLATION])

diff -r e6df770c0e58 -r 8b26adf64adc BSseeker2/galaxy/bs_seeker2_wrapper.xml
--- a/BSseeker2/galaxy/bs_seeker2_wrapper.xml Fri Jul 12 18:47:28 2013 -0400
+++ b/BSseeker2/galaxy/bs_seeker2_wrapper.xml Tue Nov 05 01:55:39 2013 -0500

[

b'@@ -1,255 +1,270 @@\n-<tool id="bs_seeker_wrapper" name="BS-Seeker2" version="2.0.0">\n- <requirements><requirement type=\'package\'>bs_seeker2</requirement></requirements>\n- <description>Versatile aligner for bisulfite sequencing data</description>\n- <command interpreter="python">\n- bs_seeker2_wrapper.py\n- ### define exec path\n- ### --exec-path "/u/home/galaxy/galaxy/GalaxyTools/bin"\n- ### [Please change the following path to your local directory]\n- --exec-path "/Users/weilong/Documents/program/BSseeker2"\n- ### output\n- --align--output $align_output\n- --call_methylation--wig $call_methylation_wig\n- --call_methylation--CGmap $call_methylation_CGmap\n- --call_methylation--ATCGmap $call_methylation_ATCGmap\n- --call_methylation--txt\n-\n- #if $singlePaired.sPaired == "paired"\n- --align--input_1 $input1\n- --align--input_2 $singlePaired.input2\n- #end if\n-\n-\n- ### aligner\n- --align--aligner ${choosealigner.aligner}\n-\n- ### Index from history or built-in\n- #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"\n- --build--file ${choosealigner.rrbsFragments.refGenomeSource.ownFile}\n- --build--aligner ${choosealigner.aligner}\n- --align-g ${choosealigner.rrbsFragments.refGenomeSource.ownFile}\n- --align--db ${choosealigner.rrbsFragments.refGenomeSource.ownFile}\n- #else if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "indexed"\n- --align--db ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}\n- --align-g ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}/${choosealigner.rrbsFragments.refGenomeSource.index.fields.dbkey}.fa\n-\n- #end if\n-\n- ### RRBS or WGBS\n- #if $choosealigner.rrbsFragments.Fragmented == "Yes"\n- #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"\n- --build--rrbs\n- --build--low ${choosealigner.rrbsFragments.lowerBound}\n- --build--up ${choosealigner.rrbsFragments.upperBound}\n- #end if\n- --align--rrbs\n- --align--low ${choosealigner.rrbsFragments.lowerBound}\n- --align--up ${choosealigner.rrbsFragments.upperBound}\n- #end if\n-\n-\n-\n- ### Inputs\n- #if $singlePaired.sPaired == "single"\n- --align-i $input1\n- #end if\n-\n- ### Library type\n- --align-t $tag\n-\n- ### other general options\n- #if $sParams.sSettingsType == "preSet"\n- --align--start_base 1\n- --align--end_base 200\n- --align--mis 4\n- #end if\n-\n- ### adapter information\n- #if $adapterInfo.useAdapter == "Yes"\n- --align--adapter ${adapterInfo.adapter_file}\n- #end if\n-\n- #if $sParams.sSettingsType == "full"\n- --align--start_base ${sParams.start_base}\n- --align--end_base ${sParams.end_base}\n- --align--mis ${sParams.num_mismatch}\n- #end if\n-\n- </command>\n- <inputs>\n- <param format="fastq,fasta,qseq" name="input1" type="data" label="Input your read file" help="reads file in fastq, qseq or fasta format" />\n- <conditional name="singlePaired">\n- <param name="sPaired" type="select" label="Is this library mate-paired?">\n- <option value="single">Single-end</option>\n- <option value="paired">Paired-end</option>\n- </param>\n- <when value="paired">\n- <param format="fastq,fasta,qseq" name="input2" type="data" label="Input your read file 2" help="reads in fastq, qseq or fasta format" />\n- <param name="min_ins_distance" type="integer" value="-1" label=" Minimum insert size for valid paired-end alignments" />\n- <param name="max_ins_distance" type="integer" value="400" label="Maximum insert size for valid paired-end alignments" />\n- </when>\n- </conditional> \n- <param name="tag" type="select" label="Type of librar'..b'" label="Will you select a reference genome from your history or use a built-in index?" help="">\r\n+ <option value="indexed">Use a built-in index</option>\r\n+ <option value="history">Use one from the history</option>\r\n+ </param>\r\n+ <when value="indexed">\r\n+ <param name="index" type="select" label="Select a reference genome (WGBS, bowtie2)">\r\n+ <options from_data_table="bs_seeker2_indexes_WGBS_bowtie2">\r\n+ <filter type="sort_by" column="2"/>\r\n+ <validator type="no_options" message="No indexes are available for the selected input dataset"/>\r\n+ </options>\r\n+ </param>\r\n+ </when>\r\n+ <when value="history">\r\n+ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />\r\n+ </when>\r\n+ </conditional>\r\n+ </when>\r\n+ </conditional>\r\n+\r\n+\r\n+ <conditional name="mode_type">\r\n+ <param name="mode" type="select" label="Select the mode of Bowtie2">\r\n+ <option value="local" selected="true"> local alignment </option>\r\n+ <option value="end_to_end" > end-to-end alignment </option>\r\n+ </param>\r\n+ </conditional>\r\n+ </when>\r\n+ </conditional>\r\n+ <conditional name="adapterInfo">\r\n+ <param name="useAdapter" type="select" label="adapter sequence">\r\n+ <option value="noAdapter">No</option>\r\n+ <option value="withAdapter">Yes</option>\r\n+ </param>\r\n+ <when value="withAdapter">\r\n+ <param format="txt" name="adapter_file" type="data" label="Input file of your adaptor sequences" help="Input text file of your adaptor sequences" />\r\n+ </when>\r\n+ </conditional>\r\n+\r\n+ <conditional name="sParams">\r\n+ <param name="sSettingsType" type="select" label="BS Seeker2 settings to use" help="You can use the default settings or set customer values for the BS Seeker2 parameters.">\r\n+ <option value="preSet">User Defaults</option>\r\n+ <option value="full">Full parameter list</option>\r\n+ </param>\r\n+ <when value="preSet" /> \r\n+ <when value="full">\r\n+ <param name="start_base" type="integer" value="1" label="The start base of the read to be mapped" help="" />\r\n+ <param name="end_base" type="integer" value="200" label="The end base of the read to be mapped" help="" />\r\n+\r\n+ <param name="num_mismatch" type="integer" value="4" label="Number of mismatches" help="(INT) Default: 4" />\r\n+ </when> \r\n+ </conditional>\r\n+\r\n+</inputs>\r\n+\r\n+ <outputs>\r\n+ <data format="bam" name="align_output" label="BAM Alignments"> </data>\r\n+ <data format="wig" name="call_methylation_wig" label="Methylation Levels"> </data>\r\n+ <data format="tabular" name="call_methylation_CGmap" label="CGmap file"> </data>\r\n+ <data format="tabular" name="call_methylation_ATCGmap" label="ATCGmap file"> </data>\r\n+\r\n+ </outputs>\r\n+ <help>\r\n+**What it does**\r\n+\r\n+BS-Seeker2 is a seamlessly pipeline for mapping bisulfite sequencing data and generating detailed DNA methylome. BS-Seeker2 improves mappability by using local alignment, and is tailored for RRBS library by building special index, with higher efficiency and accuracy. This is the Galaxy version of BS-Seeker2.\r\n+\r\n+------\r\n+\r\n+**Resources**\r\n+\r\n+The homepage for BS-Seeker2 is http://pellegrini.mcdb.ucla.edu/BS_Seeker2/.\r\n+\r\n+For more information of BS-Seeker2, please refer to https://github.com/BSSeeker/BSseeker2.\r\n+\r\n+------\r\n+\r\n+**Example**\r\n+\r\n+- Adapter file::\r\n+\r\n+ AGATCGGAAGAGCACACGTC\r\n+\r\n+\r\n+ </help>\r\n+</tool>\r\n'