Builds removed

	deleted:    build/lib/fatool/__init__.py
	deleted:    build/lib/fatool/fa.py
	deleted:    build/lib/fatool/fuzzy.py
	deleted:    build/lib/fatool/sequence.py
	deleted:    build/scripts-2.7/cmdfatool.py

build/lib/fatool/__init__.py

@@ -1,3 +0,0 @@
-from .sequence import Sequence
-from .fa import Fa
-import fuzzy

build/lib/fatool/fa.py

@@ -1,216 +0,0 @@
-# -*- coding: utf-8 -*-
-
-
-import re
-import math
-from fatool import Sequence
-import logging
-
-class Fa(object):
-    def __init__(self, contigs_list, name):
-        logger = logging.getLogger(__name__)
-        
-        logger.debug('creating Fa object')
-        self.name = name
-        self.contigs = []
-        self.contigs_idx = {}
-        for r in contigs_list:
-            if not isinstance(r, Sequence):
-                logger.error('Supplied param is not Sequence object')
-                raise TypeError('Wrong param supplied Sequence was expected')
-            if not r.name in self.contigs_idx:
-                if len(self.contigs) > 0:
-                    logger.debug('appending contig: '+r.name)
-                    self.contigs.append(r)
-                else:
-                    logger.debug('adding first contig: '+r.name)
-                    self.contigs = [r]
-
-                self.contigs_idx[r.name] = len(self.contigs) - 1
-            else:
-                logger.error('Sequence name: '+r.name+' already exists in file')
-                raise NameError('Sequence name already exists: '+r.name)
-            
-            
-    @staticmethod
-    def load_from_file(file):
-        if isinstance(file, str):
-            with open(file, 'r') as f:
-                contigs = Fa.load_content(f.read())
-                name = file
-        else:
-            name = file.name
-            with file as f:
-                contigs = Fa.load_content(f.read() )
-                
-                
-        return Fa(contigs, name)
-            
-    @staticmethod       
-    def load_content(content):
-        #print content
-        nc = content.split('>')
-        contigs_list = []
-        for r in nc[1:]:
-            contigs_list.append(Sequence('>'+r.split('\n', 1)[0], re.sub('^>.*\n', '', '>'+r.rstrip())))
-        return contigs_list
-
-    def write(self, fafile):
-        if isinstance(fafile, str):
-            with open(fafile, 'w') as f:
-                f.write(str(self))
-        else:
-            with fafile as f:
-                f.write(str(self))
-
-    def write_multiple_files(self, dir):
-        dir = dir.rstrip('/')
-        dir = dir.rstrip('\\')
-        if len(dir) > 0:
-            dir = dir+'/'
-        for r in self.contigs:
-            with open(dir+r.name+'.fa', 'w') as w:
-                w.write(str(r))
-
-    def add_contigs(self, contig_list, owrite=0):
-        for r in contig_list:
-            self.add_contig(r, owrite)
-
-
-    def add_contig(self, contig, owrite = 0):
-        if not isinstance(contig, Sequence):
-            raise TypeError('Wrong param supplied contig was expected')
-        if contig.name in self.contigs_idx:
-            if owrite == 1:
-                #rem old item and add new name
-                del self.contigs[self.contigs_idx[contig.name]]
-                self.contigs.append(contig)
-                for a, r in enumerate(self.contigs):
-                    #print 'cnt '+str(r)
-                    self.contigs_idx[r.name] = a
-        else:
-            self.contigs.append(contig)
-            self.contigs_idx[contig.name] = len(self.contigs) - 1
-
-    def show_names(self):
-        return sorted(self.contigs_idx, key=self.contigs_idx.get)
-        
-    
-    def extract(self, contigs_name_list):
-        new_contig_list = []
-        for r in contigs_name_list:
-            if r in self.contigs_idx:
-                new_contig_list.append(self.contigs[self.contigs_idx[r]])
-        return Fa(new_contig_list, 'extr_'+self.name)
-
-    def remove(self, contigs_name_list):
-        new_contig_list = []
-        for r in self.contigs:
-            if not r.name in contigs_name_list:
-                new_contig_list.append(r)
-        return Fa(new_contig_list, 'rem_'+self.name)
-
-    def validate(self):
-        '''
-        '''
-
-    def nl_statistics(self, g, percent):
-        '''
-        Counts statistics of N50, L50, N75 etc.
-        g array containing sorted contigs by length, from biggest to lowest
-        '''
-        ncount = -1 # index & number of contigs with +1
-        nsum = 0
-        stop = math.floor(self.stats['L']*(percent/100.00))
-        while nsum < stop:
-            ncount += 1
-            nsum += g[ncount]
-            
-        self.stats['N'+str(percent)] = g[ncount]
-        self.stats['L'+str(percent)] = ncount + 1
-
-    def bp_stats(self, length):
-        self.stats['totalc'] += 1
-        if length > 50000:
-            self.stats['nbp50000'] += 1  # number of contigs with length
-            self.stats['lbp50000'] += length  # total length of contigs with min. len
-        elif length > 25000:
-            self.stats['nbp25000'] += 1
-            self.stats['lbp25000'] += length
-        elif length > 10000:
-            self.stats['nbp10000'] += 1
-            self.stats['lbp10000'] += length
-        elif length > 5000:
-            self.stats['nbp5000'] += 1
-            self.stats['lbp5000'] += length
-        elif length > 1000:
-            self.stats['nbp1000'] += 1
-            self.stats['lbp1000'] += length
-        
-    def statistics(self):
-        self.stats = {
-            'A': 0, 'C': 0, 'T': 0, 'G': 0, 'N': 0, 'L': 0,
-            'nbp1000': 0, 'nbp5000': 0, 'nbp10000': 0, 'nbp25000': 0, 'nbp50000': 0,
-            'lbp1000': 0, 'lbp5000': 0, 'lbp10000': 0, 'lbp25000': 0, 'lbp50000': 0,
-            'totalc':0
-        }
-        nstat_list = []
-        bp_stats = []
-        for r in self.contigs:
-            temp = r.statistics()
-            self.stats['A'] += temp['A']
-            self.stats['C'] += temp['C']
-            self.stats['T'] += temp['T']
-            self.stats['G'] += temp['G']
-            self.stats['N'] += temp['N']
-            self.stats['L'] += temp['L']
-            nstat_list.append(temp['L'])
-            self.bp_stats(temp['L'])
-
-        self.stats['longest'] = max(nstat_list)
-        nstat_list.sort()
-        nstat_list.reverse()
-
-        self.nl_statistics(nstat_list, 50)
-        self.nl_statistics(nstat_list, 75)
-        self.nl_statistics(nstat_list, 90)
-        
-        #print self.stats
-        
-        return self.stats
-
-    def sort(self, mono):
-        contig_list = []
-        temp = {}  # dict to store name:len(contig)
-        for r in self.contigs:
-            temp[r.name] = len(r)
-
-        if mono == -1:
-            for r in sorted(temp, key=temp.get)[::-1]:
-                contig_list.append(self.contigs[self.contigs_idx[r]])
-        else:
-            for r in sorted(temp, key=temp.get):
-                contig_list.append(self.contigs[self.contigs_idx[r]])
-
-        return Fa(contig_list, 'sorted_'+self.name)
-    
-    def reverse():
-        cl = []
-        for r in self.contigs:
-            cl.append(r.reverse)
-        return Fa(cl, 'rev_'+self.name)
-    
-    def join(self, fa_list, owrite = 0):
-        for fa in fa_list:
-            if not isinstance(fa, Fa):
-                raise TypeError('Wrong param supplied Fa was expected')
-            self.add_contigs(fa.contigs, owrite)
-            
-    def count_contigs(self):
-        return len(self.contigs)
-
-    def __str__(self):
-        return_string = ''
-        for r in self.contigs:
-            return_string += str(r)
-        return return_string

build/lib/fatool/fuzzy.py

@@ -1,93 +0,0 @@
-# -*- coding: utf-8 -*-
-
-#import math
-import logging
-
-def find_aprox_match_iter(needle, hstack, missmatch_level, hs_start_pos = 0):
-    i = hs_start_pos # start iterate from start position 
-    start = hs_start_pos # start of founded region at begining start of search
-    mmatch_count = 0  # missmatch counter
-    needle_len = len(needle)
-    j = 0  # needle iterator
-    while i < len(hstack):
-        if hstack[i] != needle[j]:
-            mmatch_count += 1
-            if mmatch_count > missmatch_level:
-            # if missmatch level oversized back to strat + 1 and start again
-                i -= j
-            # needle iterator restart (-1) because it will be increased in a moment
-                j = -1
-            # new start = start + 1
-                start = i+1
-                #print 'start = '+str(start)
-            # reset mmatch_count
-                mmatch_count = 0
-        i += 1
-        j += 1
-        # if needle iterator = len of needle match found return it.
-        if j >= needle_len:
-            return (start,i,mmatch_count)
-            
-def find_all_aprox_matches(needle, hstack, missmatch_level, hs_start_pos):
-    ret_list = [] # list of matches to return
-    i = hs_start_pos # start iteration from start position
-    needle_len = len(needle)
-    while i+needle_len <= len(hstack):
-        r = find_aprox_match_iter(needle, hstack, missmatch_level, i)
-        # match found append to list strat new look in start + 1 position
-        if r:
-            ret_list.append(r)
-            i = r[0]+1
-        # match not found - no more maches in hstack
-        else:
-            break
-    return ret_list
-
-# return string from between two aproximated motifs 
-def find_motif_in_aprox_range(start_motif, stop_motif, hstack, missmatch_level, hs_start_pos = 0):
-    start = 0
-    stop = 0
-    start = find_aprox_match_iter(start_motif, hstack, missmatch_level, hs_start_pos = 0)
-    stop = find_aprox_match_iter(stop_motif, hstack, missmatch_level, start[1])
-    if start and stop:
-        return hstack[start[1]:stop[0]]
-        
-def find_all_motifs_in_aprox_range(start_motif, stop_motif, hstack, missmatch_level, hs_start_pos = 0, len_min = 0, len_max = float('inf')):
-    i = hs_start_pos
-    start = 0
-    stop = 0
-    ret_list = []
-    logger = logging.getLogger(__name__)
-    #logger.setLevel(logging.DEBUG)
-    logger.debug([start_motif, stop_motif, hstack, missmatch_level, hs_start_pos, len_min, len_max])
-    logger.debug(hstack)
-    
-    while i <= len(hstack):
-        start = find_aprox_match_iter(start_motif, hstack, missmatch_level, i)
-        stop = find_aprox_match_iter(stop_motif, hstack, missmatch_level, start[1])
-        if start and stop:
-            if stop[1] - start[0] >= len_min and stop[1] - start[0] <= len_max:
-                ret_list.append(hstack[start[0]:stop[1]])
-            i = start[0]+1
-        else:
-            break
-    logger.debug(ret_list)
-    return ret_list
-
-def find_motif(needle, hstack, missmatch_level, hs_start_pos = 0):
-    r = 0
-    r = find_aprox_match_iter(needle, hstack, missmatch_level, hs_start_pos = 0)
-    if r:
-        return hstack[r[0]:r[1]]
-
-def find_all_motifs(needle, hstack, missmatch_level, hs_start_pos = 0):
-    i = hs_start_pos
-    ret_list = []
-    while i <= len(hstack):
-        r = find_aprox_match_iter(needle, hstack, missmatch_level, i )
-        if r:
-            ret_list.append(hstack[r[0]:r[1]])
-            i = r[0]+1
-        else:
-            break
-    return ret_list