--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_extract_sequence_file.py	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,414 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+import argparse
+import copy
+import operator
+
+FASTA_FILE_LAST_POS = None
+
+#################
+# Parse methods #
+#################
+def text_end_of_file(row):
+    if row == '':
+        return True
+    else:
+        return False
+
+def get_new_line(input_file, generate_error = True):
+    row = input_file.readline()
+    if text_end_of_file(row):
+        if generate_error :
+            string = os.path.basename(__file__) + ': '
+            string += ' unexpected end of file'
+            raise ValueError(string)
+        else :
+            return None
+    else:
+        return row[:-1]
+
+def next_fasta_record(input_file):
+    global FASTA_FILE_LAST_POS
+    if FASTA_FILE_LAST_POS != None:
+        input_file.seek(FASTA_FILE_LAST_POS)
+    else:
+        FASTA_FILE_LAST_POS = input_file.tell()
+
+    id_line = get_new_line(input_file, generate_error = False)
+    if id_line == None:
+        return None
+    split_line = id_line[1:].split(' ')
+    seq_id = split_line[0]
+    description = ' '.join(split_line[1:])
+    new_line = get_new_line(input_file, generate_error = False)
+    seq = ''
+    while new_line != None:
+        if new_line[0] != '>':        
+            seq += new_line
+            FASTA_FILE_LAST_POS = input_file.tell()
+            new_line = get_new_line(input_file, generate_error = False)
+        else:
+            new_line = None
+    return SeqRecord(seq_id, seq, description)
+
+def next_fastq_record(input_file):
+    id_line = get_new_line(input_file, generate_error = False)
+    if id_line == None:
+        return None
+    if id_line[0] != '@':
+        string = os.path.basename(__file__) + ': '
+        string += ' issue in fastq file'
+        raise ValueError(string)
+    split_line = id_line[1:].split(' ')
+    seq_id = split_line[0]
+    description = ' '.join(split_line[1:])
+    seq = get_new_line(input_file)
+    spacer = get_new_line(input_file)
+    quals = get_new_line(input_file)
+    return SeqRecord(seq_id, seq, description, quals)
+
+def next_record(input_file, file_format):
+    if file_format == 'fasta':
+        return next_fasta_record(input_file)
+    elif file_format == 'fastq':
+        return next_fastq_record(input_file)
+    else:
+        string = os.path.basename(__file__) + ': '
+        string += file_format + ' is not managed'
+        raise ValueError(string)
+
+def write_fasta_record(record, output_sequence_file):
+    output_sequence_file.write('>' + record.get_id() + ' ' + 
+        record.get_description() + '\n')
+    seq = record.get_sequence()
+    split_seq = [seq[i:i+60] for i in xrange(0,len(seq),60)]
+    for split in split_seq:
+        output_sequence_file.write(split + '\n')
+
+def format_qual_value(qual_score, sliding_value, authorized_range, qual_format):
+    ascii_value = ord(qual_score)
+    score = ascii_value-sliding_value
+    if score < authorized_range[0] or score > authorized_range[1]:
+        string = os.path.basename(__file__) + ': wrong score ('
+        string += str(score) + ') with quality format ('
+        string += qual_format
+        raise ValueError(string)
+    return score
+
+def format_qual_string(qual_string, qual_format):
+    if qual_format == 'sanger':
+        return format_qual_value(qual_string, 33 ,[0,40], qual_format)
+    elif qual_format == "solexa":
+        return format_qual_value(qual_string, 64 ,[-5,40], qual_format)
+    elif qual_format == "illumina_1_3":
+        return format_qual_value(qual_string, 33 ,[0,40], qual_format)
+    elif qual_format == "illumina_1_5":
+        return format_qual_value(qual_string, 33 ,[3,40], qual_format)
+    elif qual_format == "illumina_1_8":
+        return format_qual_value(qual_string, 33 ,[0,41], qual_format)
+    else:
+        string = os.path.basename(__file__) + ': quality format ('
+        string += qual_format + ') is not managed'
+        raise ValueError(string) 
+
+def write_qual_record(record, output_qual_file, qual_format):
+    output_qual_file.write('>' + record.get_id() + ' ' + 
+        record.get_description() + '\n')
+    qual = record.get_quality()
+    qual = [str(format_qual_string(qual_str,qual_format)) for qual_str in qual]
+    split_seq = [qual[i:i+60] for i in xrange(0,len(qual),60)]
+    for split in split_seq:
+        output_qual_file.write(' '.join(split) + '\n')
+
+def write_fastq_record(record, output_sequence_file):
+    output_sequence_file.write('@' + record.get_id() + ' ' + 
+        record.get_description() + '\n')
+    output_sequence_file.write(record.get_sequence() + '\n')
+    output_sequence_file.write('+\n')
+    output_sequence_file.write(record.get_quality() + '\n')
+
+def write_information(record, output_file_formats, output_sequence_file, 
+    output_qual_file, qual_format):
+    if "fasta" in output_file_formats:
+        write_fasta_record(record, output_sequence_file)
+    if "qual" in output_file_formats:
+        write_qual_record(record, output_qual_file, qual_format)
+    if "fastq" in output_file_formats:
+        write_fastq_record(record, output_sequence_file)
+
+def fast_test_element_in_list(element,list_to_test):
+    to_continue = True
+    i = 0
+    while to_continue:
+        if i == len(list_to_test) or list_to_test[i] >= element:
+            to_continue = False
+        else:
+            i += 1
+
+    found = False
+    if i < len(list_to_test):
+        if list_to_test[i] == element:
+            found = True
+
+    return found
+
+#########################
+# Constraint definition #
+#########################
+constraints = {
+    'equal': operator.eq,
+    'different': operator.ne,
+    'lower': operator.le,
+    'strictly_lower': operator.lt,
+    'greater': operator.ge,
+    'strictly_greater': operator.gt,
+    'in': operator.contains,
+    'not_in': 'in'
+}
+
+extractable_information = {
+    'id': str,
+    'length': int,
+    'description': str
+}
+
+###########
+# Classes #
+###########
+class SeqRecord:
+
+    def __init__(self, seq_id, sequence, description, quality = ""):
+        self.id = seq_id
+        self.sequence = sequence
+        self.quality = quality
+        self.description = description
+        self.length = len(self.sequence)
+
+    # Getters
+    def get_id(self):
+        return self.id
+
+    def get_sequence(self):
+        return self.sequence
+
+    def get_quality(self):
+        return self.quality
+
+    def get_length(self):
+        return self.length
+
+    def get_description(self):
+        return self.description
+
+    def get(self, category):
+        if category == 'id':
+            return self.get_id()
+        elif category == 'length':
+            return self.get_length()
+        elif category == 'description':
+            return self.get_description()
+        else:
+            string = os.path.basename(__file__) + ': '
+            string += category + ' can not be extracted from SeqRecord'
+            raise ValueError(string)
+
+    # Other functions
+    def extract_information(self,to_extract):
+        extracted_info = []
+        for info_to_extract in to_extract:
+            extracted_info.append(self.get(info_to_extract))
+        return extracted_info
+
+    def test_conservation(self, constraints):
+        to_conserve = True
+        for constrained_info in constraints:
+            record_value = self.get(constrained_info)
+            for constraint in constraints[constrained_info]:
+                to_conserve &= constraint.test_constraint(record_value)
+        return to_conserve
+
+class Records:
+
+    def __init__(self, input_filepath, file_format, constraints):
+        self.records = []
+        self.conserved_records = []
+        with open(input_filepath, 'r') as input_file:
+            to_continue = True
+            while to_continue:
+                record = next_record(input_file, file_format)
+                if record != None:
+                    self.records.append(record)
+                    to_conserve = record.test_conservation(constraints)
+                    if to_conserve:
+                        self.conserved_records.append(copy.copy(record))
+                else:
+                    to_continue = False           
+
+    # Getters
+    def get_records(self):
+        return copy.copy(self.records)
+
+    def get_record_nb(self):
+        return len(self.records)
+
+    def get_conserved_records(self):
+        return copy.copy(self.conserved_records)
+
+    def get_conserved_record_nb(self):
+        return len(self.conserved_records)
+
+    # Other functions
+    def save_conserved_records(self,args):
+        if args.custom_extraction_type == 'True':
+            to_extract = args.to_extract[1:-1].split(',')
+            with open(args.output_information, 'w') as output_information_file:
+                output_information_file.write('\t'.join(to_extract) + '\n')
+                for record in self.conserved_records:
+                    extracted_info = record.extract_information(to_extract)
+                    string_info = [str(info) for info in extracted_info]
+                    string = '\t'.join(string_info)
+                    output_information_file.write(string + '\n')
+        else:
+            qual_format = None
+            if args.format == 'fasta':
+                output_file_formats = ['fasta']
+            elif args.format == 'fastq':
+                if args.split == 'True':
+                    output_file_formats = ['fasta','qual']
+                    qual_format = args.quality_format
+                else:
+                    output_file_formats = ['fastq']
+
+            with open(args.output_sequence,'w') as output_sequence_file: 
+                if "qual" in output_file_formats:
+                    output_qual_file = open(args.output_quality, 'w')
+                else:
+                    output_qual_file = None
+                for record in self.conserved_records:
+                    write_information(record, output_file_formats,
+                        output_sequence_file, output_qual_file, qual_format)
+                if "qual" in output_file_formats:
+                    output_qual_file.close()
+
+class Constraint:
+
+    def __init__(self, constraint_type, value, constrained_information):
+        if not constraints.has_key(constraint_type):
+            string = os.path.basename(__file__) + ': '
+            string += constraint_type + ' is not a correct type of constraint'
+            raise ValueError(string)
+        self.raw_constraint_type = constraint_type
+        self.type = constraints[constraint_type]
+
+        value_format = extractable_information[constrained_information]
+        if self.raw_constraint_type in ['in', 'not_in']:
+            self.values = []
+            with open(value, 'r') as value_file:
+                for row in value_file.readlines():
+                    value = row[:-1]
+                    self.values.append(value_format(value))
+        else:
+            self.values = [value_format(value)]
+        self.values.sort()
+
+    def get_raw_constraint_type(self):
+        return self.raw_constraint_type
+
+    def get_type(self):
+        return self.type
+
+    def get_values(self):
+        return self.values
+
+    def test_constraint(self, similarity_info_value):
+        to_conserve = True
+        if self.raw_constraint_type == 'in':
+            to_conserve &= fast_test_element_in_list(similarity_info_value, 
+                self.values)
+        elif self.raw_constraint_type == 'not_in':
+            to_conserve &= (not fast_test_element_in_list(similarity_info_value, 
+                self.values))
+        else:
+            to_conserve &= self.type(similarity_info_value, self.values[0])
+        return to_conserve    
+
+################
+# Misc methods #
+################
+def test_input_filepath(input_filepath, tool, file_format):
+    if not os.path.exists(input_filepath):
+        string = os.path.basename(__file__) + ': '
+        string += input_filepath + ' does not exist'
+        raise ValueError(string)
+
+def format_constraints(constraints):
+    formatted_constraints = {}
+    if constraints != None:
+        for constr in constraints:
+            split_constraint = constr.split(': ')
+            constrained_information = split_constraint[0]
+            constraint = Constraint(split_constraint[1], split_constraint[2], 
+                constrained_information)
+            formatted_constraints.setdefault(constrained_information,[]).append(
+                constraint)
+    return formatted_constraints
+
+def convert_extract_sequence_file(args):
+    input_filepath = args.input
+    file_format = args.format
+    constraints = args.constraint
+    formatted_constraints = format_constraints(constraints)
+
+    records = Records(input_filepath, file_format, formatted_constraints)
+    records.save_conserved_records(args)
+    
+    report_filepath = args.report
+    with open(report_filepath, 'w') as report_file:
+
+        report_file.write('Information to extract:\n')
+        if args.custom_extraction_type == 'True':
+            for info in args.to_extract[1:-1].split(','):
+                report_file.write('\t' + info + '\n')
+        else:
+            report_file.write('\tsequences\n')
+
+        if constraints != None:
+            report_file.write('Constraints on extraction:\n')
+            for constrained_info in formatted_constraints:
+                report_file.write('\tInfo to constraint: ' + constrained_info 
+                    + '\n')
+                for constraint in formatted_constraints[constrained_info]:
+                    report_file.write('\t\tType of constraint: ' + 
+                        constraint.get_raw_constraint_type()
+                        + '\n')
+                    report_file.write('\t\tValues:\n')
+                    values = constraint.get_values()
+                    for value in values:
+                        report_file.write('\t\t\t' + str(value) + '\n')
+        report_file.write('Number of similarity records: ' + 
+            str(records.get_record_nb()) + '\n')
+        report_file.write('Number of extracted similarity records: ' +
+            str(records.get_conserved_record_nb()) + '\n')
+
+########
+# Main #
+########
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input', required=True)
+    parser.add_argument('--format', required=True)
+    parser.add_argument('--custom_extraction_type', required=True)
+    parser.add_argument('--to_extract')
+    parser.add_argument('--output_information')
+    parser.add_argument('--split')
+    parser.add_argument('--quality_format')
+    parser.add_argument('--output_sequence')
+    parser.add_argument('--output_quality')
+    parser.add_argument('--constraint', action='append')
+    parser.add_argument('--report', required=True)
+    args = parser.parse_args()
+
+    convert_extract_sequence_file(args)