Updating proBAM_pepxml.py: fixing the function get_enzyme_pepxml() in…

python/proBAM_biomart.py

@@ -17,59 +17,72 @@
 
 from __future__ import division
 
+from bioservices import BioMart
+
 __author__ = 'Volodimir Olexiouk'
 
-from bioservices import BioMart
 
 #
 #Function that links the correct database archive with version number
 #
-def _get_ensembl_archive_(version,species):
+def _get_ensembl_archive_(version, species):
     '''
     :param version: Ensembl version
     :return: ENSEMBL repository for a specific version
     '''
-    version=int(version)
-    if species=='arabidopsis_thaliana':
+    version = int(version)
+    if species == 'arabidopsis_thaliana':
         return 'plants.ensembl.org'
     else:
-        d={}
-        d[89]="www.ensembl.org"
-        d[88]="mar2017.archive.ensembl.org"
-        d[87]="dec2016.archive.ensembl.org"
-        d[86]="oct2016.archive.ensembl.org"
-        d[85]="jul2016.archive.ensembl.org"
-        d[84]="mar2016.archive.ensembl.org"
-        d[83]="dec2015.archive.ensembl.org"
-        d[82]="sep2015.archive.ensembl.org"
-        d[81]="jul2015.archive.ensembl.org"
-        d[80]="may2015.archive.ensembl.org"
-        d[79]="mar2015.archive.ensembl.org"
-        d[78]="dec2014.archive.ensembl.org"
-        d[77]="oct2014.archive.ensembl.org"
-        d[76]="aug2014.archive.ensembl.org"
-        d[75]="feb2014.archive.ensembl.org"
-        d[74]="dec2013.archive.ensembl.org"
-        d[73]="sep2013.archive.ensembl.org"
-        d[72]="jun2013.archive.ensembl.org"
-        d[71]="apr2013.archive.ensembl.org"
-        d[70]="jan2013.archive.ensembl.org"
-        d[69]="oct2012.archive.ensembl.org"
-        d[68]="jul2012.archive.ensembl.org"
-        d[67]="may2012.archive.ensembl.org"
-        d[66]="feb2012.archive.ensembl.org"
-        d[65]="dec2011.archive.ensembl.org"
-        d[64]="sep2011.archive.ensembl.org"
-        d[63]="jun2011.archive.ensembl.org"
-        d[62]="apr2011.archive.ensembl.org"
-        d[61]="feb2011.archive.ensembl.org"
-        d[60]="nov2010.archive.ensembl.org"
-        d[59]="aug2010.archive.ensembl.org"
-        d[58]="may2010.archive.ensembl.org"
-        d[57]="mar2010.archive.ensembl.org"
-        d[56]="sep2009.archive.ensembl.org"
-        d[55]="jul2009.archive.ensembl.org"
-        d[54]="may2009.archive.ensembl.org"
+        d = {}
+        d[101] = "www.ensembl.org"
+        d[100] = "apr2020.archive.ensembl.org"
+        d[99] = "jan2020.archive.ensembl.org"
+        d[98] = "sep2019.archive.ensembl.org"
+        d[97] = "jul2019.archive.ensembl.org"
+        d[96] = "apr2019.archive.ensembl.org"
+        d[95] = "jan2019.archive.ensembl.org"
+        d[94] = "oct2018.archive.ensembl.org"
+        d[93] = "jul2018.archive.ensembl.org"
+        d[92] = "apr2018.archive.ensembl.org"
+        d[91] = "dec2017.archive.ensembl.org"
+        d[90] = "aug2017.archive.ensembl.org"
+        d[89] = "may2017.archive.ensembl.org"
+        d[88] = "mar2017.archive.ensembl.org"
+        d[87] = "dec2016.archive.ensembl.org"
+        d[86] = "oct2016.archive.ensembl.org"
+        d[85] = "jul2016.archive.ensembl.org"
+        d[84] = "mar2016.archive.ensembl.org"
+        d[83] = "dec2015.archive.ensembl.org"
+        d[82] = "sep2015.archive.ensembl.org"
+        d[81] = "jul2015.archive.ensembl.org"
+        d[80] = "may2015.archive.ensembl.org"
+        d[79] = "mar2015.archive.ensembl.org"
+        d[78] = "dec2014.archive.ensembl.org"
+        d[77] = "oct2014.archive.ensembl.org"
+        d[76] = "aug2014.archive.ensembl.org"
+        d[75] = "feb2014.archive.ensembl.org"
+        d[74] = "dec2013.archive.ensembl.org"
+        d[73] = "sep2013.archive.ensembl.org"
+        d[72] = "jun2013.archive.ensembl.org"
+        d[71] = "apr2013.archive.ensembl.org"
+        d[70] = "jan2013.archive.ensembl.org"
+        d[69] = "oct2012.archive.ensembl.org"
+        d[68] = "jul2012.archive.ensembl.org"
+        d[67] = "may2012.archive.ensembl.org"
+        d[66] = "feb2012.archive.ensembl.org"
+        d[65] = "dec2011.archive.ensembl.org"
+        d[64] = "sep2011.archive.ensembl.org"
+        d[63] = "jun2011.archive.ensembl.org"
+        d[62] = "apr2011.archive.ensembl.org"
+        d[61] = "feb2011.archive.ensembl.org"
+        d[60] = "nov2010.archive.ensembl.org"
+        d[59] = "aug2010.archive.ensembl.org"
+        d[58] = "may2010.archive.ensembl.org"
+        d[57] = "mar2010.archive.ensembl.org"
+        d[56] = "sep2009.archive.ensembl.org"
+        d[55] = "jul2009.archive.ensembl.org"
+        d[54] = "may2009.archive.ensembl.org"
         if version in d:
             return d[version]
         else:
@@ -84,19 +97,21 @@ def _get_ensembl_dataset_(species):
     :param species: full species name
     :return: ensembl species name
     '''
-    d={}
-    d['homo_sapiens']='hsapiens_gene_ensembl'
-    d['mus_musculus']='mmusculus_gene_ensembl'
-    d['drosophila_melanogaster']='dmelanogaster_gene_ensembl'
-    d['danio_rerio']='drerio_gene_ensembl'
-    d['arabidopsis_thaliana']='athaliana_eg_gene'
+    d = {}
+    d['homo_sapiens'] = 'hsapiens_gene_ensembl'
+    d['mus_musculus'] = 'mmusculus_gene_ensembl'
+    d['drosophila_melanogaster'] = 'dmelanogaster_gene_ensembl'
+    d['danio_rerio'] = 'drerio_gene_ensembl'
+    d['arabidopsis_thaliana'] = 'athaliana_eg_gene'
 
     if species not in d:
         print 'Error: unsupported species'
         print 'Currently supported species:'
         print d.keys()
         raise ValueError('unsupported species')
     return d[species]
+
+
 #
 # Function to create XML readable transcript_id query string
 #
@@ -105,16 +120,18 @@ def _id_in_xml_query_(transcipt_id):
     :param transcipt_id: list of transcrip IDs
     :return: XML readable transcript ID query string
     '''
-    query=""
+    query = ""
     for tr in transcipt_id:
-        query+=(str(tr)+",")
-    query=query[:-1]
+        query += (str(tr) + ",")
+    query = query[:-1]
     return query
 
+
 #
 # Function that retrieves cds,strand,chr and ensembl_transcript_id from BioMart
 #
-def retrieve_data_from_biomart(version,species,transcript_id,three_frame_translation):
+def retrieve_data_from_biomart(version, species, transcript_id,
+                               three_frame_translation):
     '''
     :param version: Database version
     :param species: Full species name
@@ -123,42 +140,44 @@ def retrieve_data_from_biomart(version,species,transcript_id,three_frame_transla
     '''
 
     #create connection
-    tr_query=_id_in_xml_query_(transcript_id)
-    version=_get_ensembl_archive_(version,species)
+    tr_query = _id_in_xml_query_(transcript_id)
+    version = _get_ensembl_archive_(version, species)
 
-    dataset=_get_ensembl_dataset_(species)
+    dataset = _get_ensembl_dataset_(species)
     biomart = BioMart(host=version)
 
     #add filters
     biomart.add_dataset_to_xml(dataset)
-    biomart.add_filter_to_xml("ensembl_transcript_id",tr_query)
+    biomart.add_filter_to_xml("ensembl_transcript_id", tr_query)
 
     #add attributes
     biomart.add_attribute_to_xml('ensembl_transcript_id')
     biomart.add_attribute_to_xml("chromosome_name")
     biomart.add_attribute_to_xml("strand")
-    if three_frame_translation=="Y":
+    if three_frame_translation == "Y":
         biomart.add_attribute_to_xml("cdna")
     else:
         biomart.add_attribute_to_xml("coding")
-    attributes=biomart.attributes(dataset)
+    attributes = biomart.attributes(dataset)
 
     #execute query
-    xml_query=biomart.get_xml()
+    xml_query = biomart.get_xml()
 
     # create bypass for plants database
-    if species=="arabidopsis_thaliana":
-        xml_query=xml_query.replace('virtualSchemaName = "default"','virtualSchemaName = "plants_mart_30"')
+    if species == "arabidopsis_thaliana":
+        xml_query = xml_query.replace('virtualSchemaName = "default"',
+                                      'virtualSchemaName = "plants_mart_30"')
 
-    result=biomart.query(xml_query)
-    result=result.split("\n")
+    result = biomart.query(xml_query)
+    result = result.split("\n")
 
     return result
 
+
 #
 # Function that maps Identifiers to ENSEMBl
 #
-def id_map_ensembl(to_annotation,version,species,psm_protein_id):
+def id_map_ensembl(to_annotation, version, species, psm_protein_id):
     '''
     :param to_annotation: target identifier annotation (i.e. uniprot_swissprot)
     :param version: Database version
@@ -167,53 +186,56 @@ def id_map_ensembl(to_annotation,version,species,psm_protein_id):
     :return: BioMart results
     '''
     # If species is in plantsDB, execute plants adjusted function
-    if species=="arabidopsis_thaliana":
-        result=id_map_ensembl_plants(to_annotation,version,species,psm_protein_id)
+    if species == "arabidopsis_thaliana":
+        result = id_map_ensembl_plants(to_annotation, version, species,
+                                       psm_protein_id)
         return result
     else:
         #adjust UniProt xml annotation for BioMart version >87
-        if int(version)>87 and "uniprot" in to_annotation:
-            to_annotation=to_annotation.replace('_','')
+        if int(version) > 87 and "uniprot" in to_annotation:
+            to_annotation = to_annotation.replace('_', '')
         #create connection
-        query_string=_id_in_xml_query_(psm_protein_id)
-        version=_get_ensembl_archive_(version,species)
-        dataset=_get_ensembl_dataset_(species)
+        query_string = _id_in_xml_query_(psm_protein_id)
+        version = _get_ensembl_archive_(version, species)
+        dataset = _get_ensembl_dataset_(species)
         biomart = BioMart(host=version)
 
         #add filters
         biomart.add_dataset_to_xml(dataset)
-        biomart.add_filter_to_xml(to_annotation,query_string)
+        biomart.add_filter_to_xml(to_annotation, query_string)
 
         #add attributs
         biomart.add_attribute_to_xml("ensembl_transcript_id")
         biomart.add_attribute_to_xml("transcript_start")
         biomart.add_attribute_to_xml("transcript_end")
         biomart.add_attribute_to_xml(to_annotation)
-        attributes=biomart.attributes(dataset)
+        attributes = biomart.attributes(dataset)
 
         #execute query
-        xml_query=biomart.get_xml()
-        tmp_result=biomart.query(xml_query)
-        if len(tmp_result)==1:
+        xml_query = biomart.get_xml()
+        tmp_result = biomart.query(xml_query)
+        if len(tmp_result) == 1:
             print "ERROR: could not convert ID's trough BioMart, " \
                   "Please check whether Ensembl version/species were correctly supplied"
-        tmp_result=tmp_result.split("\n")
-        result=[]
+        tmp_result = tmp_result.split("\n")
+        result = []
 
-        if tmp_result!=[]:
+        if tmp_result != []:
             for i in tmp_result:
-                i=i.split("\t")
-                if i[0]!="":
-                    result.append([i[0],(int(i[2])-int(i[1])),i[3]])
+                i = i.split("\t")
+                if i[0] != "":
+                    result.append([i[0], (int(i[2]) - int(i[1])), i[3]])
                 else:
                     result.append(i)
         return result
 
+
 #
 # Function that maps Identfiers to Ensembl adjusted for plant DB compatibility
 #
 
-def id_map_ensembl_plants(to_annotation,version,species,psm_protein_id):
+
+def id_map_ensembl_plants(to_annotation, version, species, psm_protein_id):
     '''
     :param to_annotation: to which annotation
     :param version: ensembl version
@@ -222,14 +244,14 @@ def id_map_ensembl_plants(to_annotation,version,species,psm_protein_id):
     :return: list of protein ID's converted to ENSEMBL
     '''
     #create connection
-    query_string=_id_in_xml_query_(psm_protein_id)
-    version=_get_ensembl_archive_(version,species)
-    dataset=_get_ensembl_dataset_(species)
+    query_string = _id_in_xml_query_(psm_protein_id)
+    version = _get_ensembl_archive_(version, species)
+    dataset = _get_ensembl_dataset_(species)
     biomart = BioMart(host=version)
 
     #add filters
     biomart.add_dataset_to_xml(dataset)
-    biomart.add_filter_to_xml(to_annotation+"_accession",query_string)
+    biomart.add_filter_to_xml(to_annotation + "_accession", query_string)
 
     #add attributs
     biomart.add_attribute_to_xml("ensembl_transcript_id")
@@ -238,17 +260,17 @@ def id_map_ensembl_plants(to_annotation,version,species,psm_protein_id):
     biomart.add_attribute_to_xml("transcript_end")
 
     #execute query
-    xml_query=biomart.get_xml()
-    xml_query=xml_query.replace('virtualSchemaName = "default"','virtualSchemaName = "plants_mart_30"')
+    xml_query = biomart.get_xml()
+    xml_query = xml_query.replace('virtualSchemaName = "default"',
+                                  'virtualSchemaName = "plants_mart_30"')
 
     #parse results and adjust length
-    temp_result=biomart.query(xml_query).split("\n")
-    result=[]
+    temp_result = biomart.query(xml_query).split("\n")
+    result = []
     for row in temp_result:
-        items=row.split("\t")
+        items = row.split("\t")
         # print row
-        if len(items)==4:
-            length=int(items[3])-int(items[1])+1
-            result.append(items[0]+"\t"+str(length)+"\t"+items[2])
+        if len(items) == 4:
+            length = int(items[3]) - int(items[1]) + 1
+            result.append(items[0] + "\t" + str(length) + "\t" + items[2])
     return result
-

python/proBAM_input.py

@@ -31,32 +31,32 @@ def get_PSM_hash(psm_file,decoy_annotation,validated_only):
     :return: dictionairy of parsed psm file,
     '''
     print "Reading PSM-file"
-    try:
+    # try:
         # catch mzid file format and parse
-        if re.match('^.*\.(mzid)$',psm_file.lower())!=None:
-            PSM=proBAM_mzid.get_PSM_mzid(psm_file,validated_only)
+    if re.match('^.*\.(mzid)$',psm_file.lower())!=None:
+        PSM=proBAM_mzid.get_PSM_mzid(psm_file,validated_only)
 
-        # catch pepxml file format and parse
-        elif re.match('^.*\.(pepxml|pep.xml|xml)$',psm_file.lower())!=None:
-            PSM=proBAM_pepxml.get_PSM_pepxml(psm_file)
+    # catch pepxml file format and parse
+    elif re.match('^.*\.(pepxml|pep.xml|xml)$',psm_file.lower())!=None:
+        PSM=proBAM_pepxml.get_PSM_pepxml(psm_file)
 
 
-        # catch mztab file format and parse
-        elif re.match('^.*\.(mztab)$',psm_file.lower())!=None:
-            PSM=proBAM_mzTab.get_PSM_mztab(psm_file)
+    # catch mztab file format and parse
+    elif re.match('^.*\.(mztab)$',psm_file.lower())!=None:
+        PSM=proBAM_mzTab.get_PSM_mztab(psm_file)
 
-        else:
-            raise IOError('Unrecognized file extension, \n ' \
-                  'Accepted file extensions: .mzid/.pepxml/.pep.xml/.xml')
+    else:
+        raise IOError('Unrecognized file extension, \n ' \
+              'Accepted file extensions: .mzid/.pepxml/.pep.xml/.xml')
 
-    except Exception as e:
-        print "ERROR: Unable to  the PSM file : \n"
-        print e.__doc__
-        print e.message
-        print "\nPlease confirm that the file is conform with the document specification." \
-              "If the error keeps occuring contact the developers at https://github.com/Biobix/proBAMconvert/issues " \
-              "and supply this error message along with the file and used settings"
-        raise IOError()
+    # except Exception as e:
+    #     print "ERROR: Unable to  the PSM file : \n"
+    #     print e.__doc__
+    #     print e.message
+    #     print "\nPlease confirm that the file is conform with the document specification." \
+    #           "If the error keeps occuring contact the developers at https://github.com/Biobix/proBAMconvert/issues " \
+    #           "and supply this error message along with the file and used settings"
+    #     raise IOError()