single_feature.py

#! /usr/env/bin python2.7

"""
QC functions for processing every single feature in GFF3 file.
"""
from __future__ import print_function
import re
import logging
logger = logging.getLogger(__name__)
#log.basicConfig(level=logging.DEBUG, format='%(levelname)-8s %(message)s')
logger.setLevel(logging.INFO)
if not logger.handlers:
    lh = logging.StreamHandler()
    lh.setFormatter(logging.Formatter('%(levelname)-8s %(message)s'))
    logger.addHandler(lh)
import gff3tool.lib.function4gff as function4gff
import gff3tool.lib.ERROR as ERROR


ERROR_INFO = ERROR.INFO

def FIX_PSEUDOGENE(gff):
    roots = []
    for line in gff.lines:
        try:
            if line['line_type'] == 'feature' and not line['attributes'].has_key('Parent'):
                if len(line['attributes']) != 0:
                    roots.append(line)
                else:
                    print('WARNING  [Missing Attributes] Program failed.\n\t\t- Line {0:s}: {1:s}'.format(str(line['line_index']+1), line['line_raw']))
        except KeyError:
            print('WARNING  [Missing Attributes] Program failed.\n\t\t- Line {0:s}: {1:s}'.format(str(line['line_index']+1), line['line_raw']))


    #roots = [line for line in gff.lines if line['line_type']=='feature' and not line['attributes'].has_key('Parent')]
    for root in roots:
        if root['type'] == 'pseudogene':
            for child in root['children']:
                if child['type'] == 'mRNA' or child['type'] == 'transcript':
                    child['type'] = 'pseudogenic_transcript'
                for grandchild in child['children']:
                    if grandchild['type'] == 'CDS':
                        grandchild['line_status'] = 'removed'
                    elif grandchild['type'] == 'exon':
                        grandchild['type'] = 'pseudogenic_exon'
                    others = gff.collect_descendants(grandchild)
                    for other in others:
                        other['line_status'] = 'removed'

def check_pseudogene(gff, line):
    '''
    Note:
    1. This funtion should be only applied on a gff file that has been fixed by FIX_PSEUDOGENE function.
    2. This function should be only applied on loci/transcript level features.
    '''
    eCode = 'Esf0001'
    flag = 0
    result=dict()
    try:
        for v in line['attributes'].itervalues():
            if re.search(r"[Pp][Ss][EUeu][EUeu][Dd][Oo][Gg][Ee][Nn]*", str(v)):
                flag += 1
        if flag and not re.search(r"pseudogen*", line['type']):
            result['ID'] = [line['attributes']['ID']]
            result['line_num'] = ['Line {0:s}'.format(str(line['line_index'] + 1))]
            result['eCode'] = eCode
            result['eLines'] = [line]
            result['eTag'] = ERROR_INFO[eCode]
            gff.add_line_error(line, {'message': ERROR_INFO[eCode], 'error_type': 'FEATURE_TYPE', 'eCode': eCode})
    except:
        logger.error('Program dies at Line {0:s}: {1:s}'.format(str(line['line_index']+1), line['line_raw']))
    if len(result):
        return [result]

def check_strand(gff, line):
    eCode = 'Esf0003'
    result = dict()
    try:
        if line['strand'] is '+' or line['strand'] is '-':
            pass
        elif line['strand'] is '.' or line['strand'] is '?':
            result['ID'] = [line['attributes']['ID']]
            result['line_num'] = ['Line {0:s}'.format(str(line['line_index'] + 1))]
            result['eCode'] = eCode
            result['eLines'] = [line]
            result['eTag'] = '{0:s}: legal chacracter, "{1:s}", found at the strand field'.format(ERROR_INFO[eCode], line['strand'])
            gff.add_line_error(line, {'message': ERROR_INFO[eCode], 'error_type': 'FEATURE_TYPE', 'eCode': eCode})
        else:
            result['ID'] = [line['attributes']['ID']]
            result['line_num'] = ['Line {0:s}'.format(str(line['line_index'] + 1))]
            result['eCode'] = eCode
            result['eLines'] = [line]
            result['eTag'] = '{0:s}: illegal chacracter, "{1:s}" found at the strand field'.format(ERROR_INFO[eCode], line['strand'])
            gff.add_line_error(line, {'message': ERROR_INFO[eCode], 'error_type': 'FEATURE_TYPE', 'eCode': eCode})
    except:
        logger.error('Program dies at Line {0:s}: {1:s}'.format(str(line['line_index']+1), line['line_raw']))
    if len(result):
        return [result]


def main(gff, logger=None):
    function4gff.FIX_MISSING_ATTR(gff, logger=logger)
    FIX_PSEUDOGENE(gff)


    features = [line for line in gff.lines if line['line_type']=='feature']
    error_set=list()
    for f in features:
        r = check_pseudogene(gff, f)
        if not r == None:
            error_set.extend(r)
        r = None
        r = check_strand(gff, f)
        if not r == None:
            error_set.extend(r)
        r = None

    if len(error_set):
        return(error_set)