Two new functions added.

list_files() for list all the files in the requested folder.
join_sequencing_fragments for join together sequencing fragments.

Mybiotools demo.ipynb → Demo.ipynb

@@ -206,65 +206,6 @@
     "p53.cds_seq"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "p53seq = '''GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTC\n",
-    "TAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTG\n",
-    "CTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGA\n",
-    "GCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTT\n",
-    "CCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATA\n",
-    "TTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGT\n",
-    "GGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCT\n",
-    "GTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCA\n",
-    "AGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGT\n",
-    "GCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCA\n",
-    "CAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCC\n",
-    "CTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG\n",
-    "ACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTAC\n",
-    "ATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACT\n",
-    "CCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCG\n",
-    "CACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGA\n",
-    "GCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCC\n",
-    "TTCAGATCCGTGGGCGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGC\n",
-    "CCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCT\n",
-    "ACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTGACATTCTCCACTTCTTG\n",
-    "TTCCCCACTGACAGCCTCCCACCCCCATCTCTCCCTCCCCTGCCATTTTGGGTTTTGGGTCTTTGAACCC\n",
-    "TTGCTTGCAATAGGTGTGCGTCAGAAGCACCCAGGACTTCCATTTGCTTTGTCCCGGGGCTCCACTGAAC\n",
-    "AAGTTGGCCTGCACTGGTGTTTTGTTGTGGGGAGGAGGATGGGGAGTAGGACATACCAGCTTAGATTTTA\n",
-    "AGGTTTTTACTGTGAGGGATGTTTGGGAGATGTAAGAAATGTTCTTGCAGTTAAGGGTTAGTTTACAATC\n",
-    "AGCCACATTCTAGGTAGGGGCCCACTTCACCGTACTAACCAGGGAAGCTGTCCCTCACTGTTGAATTTTC\n",
-    "TCTAACTTCAAGGCCCATATCTGTGAAATGCTGGCATTTGCACCTACCTCACAGAGTGCATTGTGAGGGT\n",
-    "TAATGAAATAATGTACATCTGGCCTTGAAACCACCTTTTATTACATGGGGTCTAGAACTTGACCCCCTTG\n",
-    "AGGGTGCTTGTTCCCTCTCCCTGTTGGTCGGTGGGTTGGTAGTTTCTACAGTTGGGCAGCTGGTTAGGTA\n",
-    "GAGGGAGTTGTCAAGTCTCTGCTGGCCCAGCCAAACCCTGTCTGACAACCTCTTGGTGAACCTTAGTACC\n",
-    "TAAAAGGAAATCTCACCCCATCCCACACCCTGGAGGATTTCATCTCTTGTATATGATGATCTGGATCCAC\n",
-    "CAAGACTTGTTTTATGCTCAGGGTCAATTTCTTTTTTCTTTTTTTTTTTTTTTTTTCTTTTTCTTTGAGA\n",
-    "CTGGGTCTCGCTTTGTTGCCCAGGCTGGAGTGGAGTGGCGTGATCTTGGCTTACTGCAGCCTTTGCCTCC\n",
-    "CCGGCTCGAGCAGTCCTGCCTCAGCCTCCGGAGTAGCTGGGACCACAGGTTCATGCCACCATGGCCAGCC\n",
-    "AACTTTTGCATGTTTTGTAGAGATGGGGTCTCACAGTGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCA\n",
-    "GGCGATCCACCTGTCTCAGCCTCCCAGAGTGCTGGGATTACAATTGTGAGCCACCACGTCCAGCTGGAAG\n",
-    "GGTCAACATCTTTTACATTCTGCAAGCACATCTGCATTTTCACCCCACCCTTCCCCTCCTTCTCCCTTTT\n",
-    "TATATCCCATTTTTATATCGATCTCTTATTTTACAATAAAACTTTGCTGCCACCTGTGTGTCTGAGGGGT\n",
-    "G'''"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "len(p53seq)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -284,7 +225,7 @@
    },
    "outputs": [],
    "source": [
-    "cleaned = mb.clean_seq(p53seq)"
+    "mb.help_info()"
    ]
   },
   {
@@ -295,7 +236,7 @@
    },
    "outputs": [],
    "source": [
-    "len(cleaned)"
+    "mb.uniprot_search('TP53')"
    ]
   },
   {
@@ -306,7 +247,7 @@
    },
    "outputs": [],
    "source": [
-    "cleaned[:20]"
+    "mb.list_files('.')"
    ]
   },
   {
@@ -317,7 +258,7 @@
    },
    "outputs": [],
    "source": [
-    "mb.reverse_complementory(cleaned[:20])"
+    "mb.list_files('.', '.pickle')"
    ]
   },
   {
@@ -328,20 +269,7 @@
    },
    "outputs": [],
    "source": [
-    "mb.primers(cleaned, length = 25)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "fragment1 = cleaned[:900]\n",
-    "fragment2 = cleaned[800:1700]\n",
-    "fragment3 = cleaned[1600:]"
+    "mb.list_files('~/Desktop/a')"
    ]
   },
   {
@@ -352,21 +280,7 @@
    },
    "outputs": [],
    "source": [
-    "fragment3"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "primers_tp53 = []\n",
-    "for fragment in [fragment1, fragment2, fragment3]:\n",
-    "    temp = mb.primers(fragment, length = 20)\n",
-    "    primers_tp53.append(temp)"
+    "mb.list_files('~/Desktop/a')"
    ]
   },
   {
@@ -377,18 +291,8 @@
    },
    "outputs": [],
    "source": [
-    "primers_tp53"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "fasta = mb.read_fasta('./sequence.fasta')"
+    "import os\n",
+    "l = os.listdir('/Users/aayangm11b/Desktop/a')"
    ]
   },
   {
@@ -399,7 +303,7 @@
    },
    "outputs": [],
    "source": [
-    "len(fasta)"
+    "l"
    ]
   },
   {
@@ -410,7 +314,8 @@
    },
    "outputs": [],
    "source": [
-    "mb.help_info()"
+    "os.chdir('/Users/aayangm11b/Desktop/a')\n",
+    "seq = mb.join_sequecning_fragments(l)"
    ]
   },
   {
@@ -421,7 +326,7 @@
    },
    "outputs": [],
    "source": [
-    "mb.uniprot_search('TP53')"
+    "len(seq)"
    ]
   },
   {

Mybiotools.py

@@ -10,6 +10,8 @@
 import urllib
 import requests
 import sys
+import os
+import os.path
 
 #instructions
 #1. html5lib is required for pandas to read table from html.
@@ -80,14 +82,60 @@ def primers(s, length = 21, f_addon = '', r_addon = ''):
 def read_fasta(path):#read a local fasta file downloaded from NCBI
     with open(path) as foo:
         return ''.join([item.strip() for item in foo.readlines()[1:]])
+
+
+def list_files(dir_name, type=None, *args):
+    '''
+    This function is used to list all the files in the requested dir. One can also get specific file types
+    by defining the type parameter.
+    The type can a string or a collection of strings that declearing file types.
+    e.g. type = '.py', type = ['.txt', '.csv', '.data']
+    '''
+    if type is None:
+        return [path for path in os.listdir(dir_name) if os.path.isfile(path)]
+    return [path for path in os.listdir(dir_name) if os.path.isfile(path) and os.path.splitext(path)[1] == type]
+
+def join_sequecning_fragments(file_list):
+    '''
+    When you send your PCR products or plasmid for sequencing, you probably get several .seq files back. 
+    Usually, one need to align these fragments with your reference sequence individually.
+    join_sequencing_fragments function provide you an easy way to get things done.
+    Prerequisits:
+    1. change working directory to the folder that contains the sequencing results
+    2. make a file list using the list_files function with type parameter set as '.seq'
+    For proper use of this function, please make sure your sequencing results are aranged in order. 
+    In other words, up stream fragments should be prior to down stream fragments.
+    '''
+    seqs = []
+    for each_file in file_list:
+        with open(each_file) as foo:
+            seq = foo.read().replace('\n', '')[100:]
+            first_N = seq.find('N')
+            if first_N <= 800:
+                seq = seq[:first_N]
+            else:
+                seq = seq[:800]
+            seqs.append(seq)
+
+    joined_seq = seqs[0]
+
+    for i in range(len(seqs)-1):
+        idx = seqs[i+1].find(seqs[i][-20:])
+        if idx == -1:
+            return 'Something wrong between %d and %d seq. Make sure your .seq files are in order.'%(i, i+1)
+        addon = seqs[i+1][idx+20:]
+        joined_seq += addon
 
+    return joined_seq
+
 
 def help_info():
     print(
         '''
-        clean_seq input_seq: remove white space or numbers in the input gene or protein sequence.
-        reverse_complementory input_seq: get the reversed complementory sequence of the input DNA sequence
-        GC_content input_seq: calculate the GC content of the input sequence
+        *clean_seq(input_seq)*: remove white space or numbers in the input gene or protein sequence.
+        *reverse_complementory(input_seq)*: get the reversed complementory sequence of the input DNA sequence.
+        *GC_content(input_seq)*: calculate the GC content of the input sequence.
+        
         --help or -h: get help info of Mybiotools
     ''')