changeset 7:0eda2c588bcd draft

Deleted selected files

--- a/blast_tool.py	Wed Oct 12 00:05:20 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,175 +0,0 @@
-"""
- Util class of BLAST API
- Use Biopython's BLAST interface to access BLAST API
- BLAST call may take more than 5 min to complete.
-
- Author Nedias  Sept, 2016
-
-"""
-
-
-# BLAST Web api, use to calling BLAST using url
-from Bio.Blast import NCBIWWW
-# BLAST XML util, use to read data from BLAST's response
-from Bio.Blast import NCBIXML
-
-
-def exec_tool(options):
-    if options.format and options.format == "fasta":
-        blast_call(options.input, options.output)
-
-
-
-
-# Call BLAST protein API
-# input: an fasta format file with polypeptide data
-# output: the searching result file from BLAST in XML format
-# return: execute status code(developing)
-def blast_call(in_file, out_file):
-
-    # Open input file(read only)
-    input_file = open(in_file, "rU")
-    # Create an output file(create or override)
-    output_file = open(out_file, "w+")
-
-    # Read all data from the input fasta file
-    fasta_string = input_file.read()
-
-    # Call BLAST to search similar protein data
-    # blastp's "p" means using the protein search API
-    # "nr" means not specific database, which will perform a search base on all possible database
-    # TODO:May consider parametrize these options
-    result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
-
-    # Read result form responded data and save them in output file
-    result = result_handle.read()
-    output_file.write(result)
-
-    return 0
-
-
-# Call BLAST protein API (text version)
-# input: polypeptide data text
-# return: the searching result from BLAST in StringIO format
-def blast_call_text(in_text):
-
-    # Call BLAST to search similar protein data
-    result_handle = NCBIWWW.qblast("blastp", "nr", in_text)
-
-    return result_handle
-
-
-# Abstract data from BLAST responded XML
-# input: the searching result file from BLAST in XML format
-# return: an dictionary include all data from BLAST result.
-#      the structure of the dictionary is:
-#      dict -- hits: Integer, number of total hits during searching
-#           -- alignments: List, alignments for all polypeptide chains(there could be many chains in a single file)
-#                |          (TODO:May consider change to dictionary and use the tag of every polypeptide chain as entry)
-#                |
-#                -- hsps: List, all high-scoring pairs(alignment) for one polypeptide chain
-#                    |
-#                    hps: Dictionary, contains all data of the high-scoring pair
-def read_blast_result(blast_xml):
-
-    # Open the BLAST result
-    result_file = open(blast_xml)
-    # Read all result using biopython
-    blast_record = NCBIXML.read(result_file)
-    # E-value limit, every data with a less-than 96% e-value will be filtered
-    E_VALUE_THRESH = 0.04
-
-    # Initialize the result dictionary
-    result_dict = dict()
-
-    # Store the hits number
-    result_dict['hits': len(blast_record.alignments)]
-    # Initialize the alignment list
-    aligns = list()
-    # Scan through all alignments
-    for alignment in blast_record.alignments:
-        # Initialize the high-score pairs list
-        hsps = list()
-        # Scan through all hsps
-        for hsp in alignment.hsps:
-            # filter all hsp has less e-value than E_VALUE_THRESH
-            if hsp.expect < E_VALUE_THRESH:
-                # Initialize high-score pair dictionary
-                hsp_dict = dict()
-                # Store all data obtained from BLAST into the dictionary
-                hsp_dict['seq'] = alignment.title
-                hsp_dict['len'] = alignment.length
-                hsp_dict['eval'] = hsp.expect
-                # Identity is calculated as the percentage of identities in the alignment
-                hsp_dict['ident'] = int(round(hsp.identities * float(100) / alignment.length))
-                hsp_dict['query'] = hsp.query
-                hsp_dict['match'] = hsp.match
-                hsp_dict['sbjct'] = hsp.sbjct
-            hsps.append(hsp_dict)
-        # Store the hsps into the alignment data
-        aligns.append(hsps)
-
-    # Store alignment data into the dictionary
-    result_dict['alignments', aligns]
-    return result_dict
-
-
-# Abstract data from BLAST responded XML (text version)
-# input: the searching result file from BLAST in StringIO
-# return: an dictionary include all data from BLAST result.
-def read_blast_result_text(blast_handle):
-
-    blast_record = NCBIXML.read(blast_handle)
-
-    E_VALUE_THRESH = 0.04
-
-    result_dict = dict()
-
-    result_dict['hits'] =  len(blast_record.alignments)
-    aligns = list()
-    for alignment in blast_record.alignments:
-        hsps = list()
-        for hsp in alignment.hsps:
-
-            if hsp.expect < E_VALUE_THRESH:
-                hsp_dict = dict()
-                hsp_dict['seq'] = alignment.title
-                hsp_dict['len'] = alignment.length
-                hsp_dict['eval'] = hsp.expect
-                hsp_dict['ident'] = int(round(hsp.identities * float(100) / alignment.length))
-                hsp_dict['query'] = hsp.query
-                hsp_dict['match'] = hsp.match
-                hsp_dict['sbjct'] = hsp.sbjct
-            hsps.append(hsp_dict)
-        aligns.append(hsps)
-
-    result_dict['alignments'] = aligns
-    return result_dict
-
-
-# Sample of usage (text version)
-def text():
-    result = blast_call_text('MTSQTTINKPGPGDGSPAGSAPAKGWRGHPWVTLVTVAVGVMMVALDGTIVAIANPAIQD\
-                            DLDASLADVQWITNAYFLALAVALITAGKLGDRFGHRQTFLIGVAGFAASSGAIGLSGSI\
-                            AAVIVFRVFQGLFGALLMPAALGLLRATFPAEKLNMAIGIWGMVIGASTAGGPILGGVLV\
-                            EHVNWQSVFFINVPVGIVAVVLGVMILLDHRAANAPRSFDVVGIVLLSASMFALVWALIK\
-                            APEWGWGSGQTWVYIGGSVVGFVLFSVWETKVKEPLIPLAMFRSVPLSAGVVLMVLMAIA\
-                            FMGGLFFVTFYLQNVHGMSPVDAGLHLLPLTGMMIVASPLAGAMITKVGPRIPLAGGMVC\
-                            TAVAMFGISTLETDTGSGLMSIWFGLLGLGLAPVMVGATEVIVGNAPMELSGVAGGLQQA\
-                            AMQIGGSLGTAVLGAVMASKVDSDLAGNWKDAGLPELTPQQADQASEAVRVGVPPVAPGT\
-                            PAEVAGKITDVAHDTFISGMSLASLVAAGVAVVAVFVAFLTKRGENAEAGAGVGHI'
-                            )
-    re_dict = read_blast_result_text(result)
-    print(re_dict['hits'])
-    for alignments in re_dict['alignments']:
-        for hsp in alignments:
-            print(hsp['seq'])
-            print(hsp['len'])
-            print(hsp['eval'])
-            print(hsp['ident'])
-            print(hsp['query'][0:75] + "...")
-            print(hsp['match'][0:75] + "...")
-            print(hsp['sbjct'][0:75] + "...")
-
-
-