CRAM support

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5ac4abc510482ee3445e5e5476fdb18f
+config: 29180893c7eadda9a872007d338d9a4c
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/index.rst.txt

@@ -35,7 +35,7 @@ In a command prompt or terminal window, run the following commands to install an
   $ bamsnap -bam test.bam -pos chr1:7364529 -out test.bam.png
 
 
-More examples and commands are available in `gallery <gallary.html>`_. Use ``-h`` to list the options available for ``bamsnap``.
+More examples and commands are available in `gallery <gallery.html>`_. Use ``-h`` to list the options available for ``bamsnap``.
 
 
 .. code:: console

docs/_build/html/_static/basic.css

@@ -693,7 +693,7 @@ pre {
     overflow-y: hidden;  /* fixes display issues on Chrome browsers */
 }
 
-pre, div[class|="highlight"] {
+pre, div[class*="highlight-"] {
     clear: both;
 }
 
@@ -704,7 +704,7 @@ span.pre {
     hyphens: none;
 }
 
-div[class^="highlight-"] {
+div[class*="highlight-"] {
     margin: 1em 0;
 }
 
@@ -764,6 +764,7 @@ div.code-block-caption code {
 }
 
 table.highlighttable td.linenos,
+span.linenos,
 div.doctest > div.highlight span.gp {  /* gp: Generic.Prompt */
     user-select: none;
 }

docs/_build/html/_static/doctools.js

@@ -285,9 +285,10 @@ var Documentation = {
   initOnKeyListeners: function() {
     $(document).keydown(function(event) {
       var activeElementType = document.activeElement.tagName;
-      // don't navigate when in search box or textarea
+      // don't navigate when in search box, textarea, dropdown or button
       if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
-          && !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) {
+          && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey
+          && !event.shiftKey) {
         switch (event.keyCode) {
           case 37: // left
             var prevHref = $('link[rel="prev"]').prop('href');

docs/_build/html/_static/pygments.css

@@ -1,5 +1,10 @@
+pre { line-height: 125%; margin: 0; }
+td.linenos pre { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+td.linenos pre.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 .highlight .hll { background-color: #ffffcc }
-.highlight  { background: #f8f8f8; }
+.highlight { background: #f8f8f8; }
 .highlight .c { color: #408080; font-style: italic } /* Comment */
 .highlight .err { border: 1px solid #FF0000 } /* Error */
 .highlight .k { color: #008000; font-weight: bold } /* Keyword */

docs/_build/html/_static/searchtools.js

@@ -59,10 +59,10 @@ var Search = {
   _pulse_status : -1,
 
   htmlToText : function(htmlString) {
-      var htmlElement = document.createElement('span');
-      htmlElement.innerHTML = htmlString;
-      $(htmlElement).find('.headerlink').remove();
-      docContent = $(htmlElement).find('[role=main]')[0];
+      var virtualDocument = document.implementation.createHTMLDocument('virtual');
+      var htmlElement = $(htmlString, virtualDocument);
+      htmlElement.find('.headerlink').remove();
+      docContent = htmlElement.find('[role=main]')[0];
       if(docContent === undefined) {
           console.warn("Content block not found. Sphinx search tries to obtain it " +
                        "via '[role=main]'. Could you check your theme or template.");
@@ -166,8 +166,7 @@ var Search = {
           objectterms.push(tmp[i].toLowerCase());
       }
 
-      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
-          tmp[i] === "") {
+      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i] === "") {
         // skip this "word"
         continue;
       }

docs/_build/html/index.html

@@ -175,7 +175,7 @@ <h2>Setting up BamSnap<a class="headerlink" href="#setting-up-bamsnap" title="Pe
 <span class="gp">$</span> bamsnap -bam test.bam -pos chr1:7364529 -out test.bam.png
 </pre></div>
 </div>
-<p>More examples and commands are available in <a class="reference external" href="gallary.html">gallery</a>. Use <code class="docutils literal notranslate"><span class="pre">-h</span></code> to list the options available for <code class="docutils literal notranslate"><span class="pre">bamsnap</span></code>.</p>
+<p>More examples and commands are available in <a class="reference external" href="gallery.html">gallery</a>. Use <code class="docutils literal notranslate"><span class="pre">-h</span></code> to list the options available for <code class="docutils literal notranslate"><span class="pre">bamsnap</span></code>.</p>
 <div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> bamsnap -h
 </pre></div>
 </div>

docs/input.rst

@@ -11,12 +11,14 @@ Alignment file
 Input files (``-bam``)
 ^^^^^^^^^^^^^^^^^^^
 
-Input files to be used can be specified using the ``-bam`` argument. It is possible to specify a single file or list multiple files.
+Input files to be used can be specified using the ``-bam`` argument. It is possible to specify a single file or list multiple files. Also, a cram file can be assigned with ``-bam`` argument.
 
 .. code:: console
 
     $ bamsnap -bam ./data/NA12878.bam
     $ bamsnap -bam ./data/NA12878.bam ./data/NA12877.bam ./data/NA12879.bam
+    $ bamsnap -bam ./data/NA12878.cram
+    $ bamsnap -bam ./data/NA12878.cram ./data/NA12877.bam ./data/NA12879.bam
 
 
 Title of bam file(s) (``-title``)
@@ -65,20 +67,21 @@ BAM list file (``-bamlist``)
     $ bamsnap -bamlist ./data/NATRIO_bamlist.txt
 
 It is possible to provide a single file listing all the input bam files to be used. The expected format is a tabular (tab-separated) file. The first column is mandatory and must contain the paths to files, the second column is optional and allows to associate labels to files.
+It also supports `.bam` and `.cram` file.
 
 .. code:: bash
 
   # example of bamlist file with lables
   ./data/NA12878.bam    NA12878 (F)
-  ./data/NA12877.bam    NA12877 (M)
+  ./data/NA12877.cram   NA12877 (M)
   ./data/NA12879.bam    NA12879 (D)
 
 
 .. code:: bash
 
   # example of bamlist file
   ./data/NA12878.bam
-  ./data/NA12877.bam
+  ./data/NA12877.cram
   ./data/NA12879.bam
 
 Genomic position

pack.sh

@@ -2,5 +2,5 @@ pip uninstall -y bamsnap
 rm -rf build
 rm -rf ./dist/*
 python3 setup.py sdist bdist_wheel
-pip install ./dist/bamsnap-0.2.14-py3-none-any.whl
+pip install ./dist/bamsnap-0.2.15-py3-none-any.whl
 # twine upload dist/*

setup.py

@@ -20,7 +20,7 @@
 }
 
 setup(name='bamsnap',
-      version='0.2.14',
+      version='0.2.15',
       url='https://github.com/danielmsk/bamsnap',
       license='MIT',
       author='Daniel Minseok Kwon',

src/bamsnap.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bamsnap
-Version: 0.2.14
+Version: 0.2.15
 Summary: A converter from .bam to .png for specific genomic region.
 Home-page: https://github.com/danielmsk/bamsnap
 Author: Daniel Minseok Kwon

src/bamsnap/_options.py

@@ -171,7 +171,7 @@ def get_options():
     confjson = util.load_json(util.getDataPath('conf.json'))
 
     parser = argparse.ArgumentParser(usage='%(prog)s <sub-command> [options]',
-                                     description='%(prog)s ver' + confjson['VERSION'] + " (" + confjson['VERSION_DATE'] + ")" + ': convert bam to image')
+                                     description='%(prog)s ver' + confjson['VERSION'] + " (" + confjson['VERSION_DATE'] + ")" + ': convert bam (or cram) to image')
     parser.add_argument('-v', '--version', action='version',
                         version='%(prog)s ver' + confjson['VERSION'] + " (" + confjson['VERSION_DATE'] + ")")
 

src/bamsnap/bam.py

@@ -6,6 +6,21 @@ def __init__(self, filename, title=''):
             self.title = title
         else:
             self.title = self.filename.split('/')[-1]
+        self.ref = None
 
     def __str__(self):
         return self.title
+
+    def getSamfileFlags(self):
+        if self.filename.endswith('.bam'):
+            return 'rb'
+        elif self.filename.endswith('.cram'):
+            return 'rc'
+        else:
+            return 'r'
+
+    def setReference(self, ref):
+        self.ref = ref
+
+    def getReference(self):
+        return self.ref

src/bamsnap/bamsnap.py

@@ -57,16 +57,25 @@ def load_bamlist(self):
                 if len(line) > 0 and line[0] != '#':
                     arr = line.split('\t')
                     if len(arr) == 2:
-                        self.bamlist.append(BAM(arr[0], arr[1]))
+                        bamObj = BAM(arr[0], arr[1])
+                        if 'ref' in self.opt:
+                            bamObj.setReference(self.opt['ref'])
+                        self.bamlist.append(bamObj)
                     else:
-                        self.bamlist.append(BAM(arr[0]))
+                        bamObj = BAM(arr[0])
+                        if 'ref' in self.opt:
+                            bamObj.setReference(self.opt['ref'])
+                        self.bamlist.append(bamObj)
         elif 'bam' in ks and len(self.opt['bam']) > 0:
             for idx, bamfile in enumerate(self.opt['bam']):
                 try:
                     title = self.opt['title'][idx]
                 except IndexError:
                     title = ""
-                self.bamlist.append(BAM(bamfile, title)) 
+                bamObj = BAM(bamfile, title)
+                if 'ref' in self.opt:
+                    bamObj.setReference(self.opt['ref'])
+                self.bamlist.append(bamObj)
 
     def start_process_drawplot(self, image_w, bamlist):
         for tno in range(self.opt['process']):
@@ -97,7 +106,7 @@ def run(self):
                 self.generate_zipfile()
 
         self.opt['log'].debug('Total running time for getting reference sequence (set_refseq): ' +
-                              str(round(timemap['set_refseq'], 3))+' sec')
+                            str(round(timemap['set_refseq'], 3))+' sec')
         self.opt['log'].info('Total running time: ' + str(round(t2-t0, 1))+' sec')
 
 

src/bamsnap/data/conf.json

@@ -1,12 +1,12 @@
 {
     "TITLE":"BAMSNAP",
-    "VERSION":"0.2.13",
-    "VERSION_DATE":"2020-09-15",
+    "VERSION":"0.2.14",
+    "VERSION_DATE":"2020-11-30",
     "PROG":"bamsnap",
     "options":[
-        {"param":"bam", "default":[], "nargs":"*", "action": null, "choices":null, "type":null, "help":"bam file(s)"},
-        {"param":"bamlist", "default":null, "nargs":null, "action":null, "choices":null, "type":null, "help":"list file with bam file paths"},
-        {"param":"title", "default":[], "nargs":"*", "action":null, "choices":null, "type":null, "help":"title (name) of bam file(s)"},
+        {"param":"bam", "default":[], "nargs":"*", "action": null, "choices":null, "type":null, "help":"bam or cram file(s)"},
+        {"param":"bamlist", "default":null, "nargs":null, "action":null, "choices":null, "type":null, "help":"list file with bam (or cram) file paths"},
+        {"param":"title", "default":[], "nargs":"*", "action":null, "choices":null, "type":null, "help":"title (name) of bam (or cram) file(s)"},
         {"param":"no_title", "default":false, "nargs":null, "action":"store_true", "choices":null, "type":null, "help":"do not draw label."},
         {"param":"title_fontsize", "default":18, "nargs":null, "action":null, "choices":null, "type":"int", "help":"font size of title"},
         {"param":"pos", "default":[], "nargs":"*", "action":null, "choices":null, "type":null, "help":"genomic position (ex. 1:816687-818057, 12:7462545)"},

src/bamsnap/drawreadset.py

@@ -163,7 +163,11 @@ class DrawReadSet():
     STRAND_GROUP_LIST = ['pos_strand', 'neg_strand']
 
     def __init__(self, bam, chrom, g_spos, g_epos, xscale, refseq="",  coverage_vaf=10):
-        self.samAlign = pysam.AlignmentFile(bam.filename, "rb")
+        self.samAlign = pysam.AlignmentFile(bam.filename, bam.getSamfileFlags())
+        if bam.filename.endswith('.cram') and bam.getReference() is not None:
+            self.samAlign = pysam.AlignmentFile(bam.filename, bam.getSamfileFlags(), reference_filename=bam.getReference())
+        else:
+            self.samAlign = pysam.AlignmentFile(bam.filename, bam.getSamfileFlags())
         self.chrom = chrom
         self.refseq = refseq
         self.g_spos = g_spos

tests/test_run.py

@@ -11,7 +11,6 @@
 
 cmdlist = []
 
-
 cmdlist.append("""
     -bam ./data/test_SV1_softclipped_1.bam \
     -title "Clipped read" \
@@ -342,18 +341,16 @@
 """)
 
 cmdlist.append("""
-    -bam ./data/test_miss_ref_chr1_944300_2.bam \
+    -bam ./data/test_miss_ref_chr1_944300_2.cram \
     -pos chr1:944315 \
     -title "test" \
-    -out ./out/test_miss_ref_chr1_944300_2.png \
+    -out ./out/test_miss_ref_chr1_944300_2_cram.png \
     -margin 50 \
     -save_image_only
 """)
 
 
 
-
-
 def test_run():
     for cmd in cmdlist:
         # cmd = cmdlist[-1]