#!/usr/bin/env python2
# Copyright 2013 by Iddo Friedberg idoerg@gmail.com
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
"""Parsers for the GAF, GPA and GPI formats from UniProt-GOA.

Uniprot-GOA README + GAF format description:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/README

GAF formats:
http://www.geneontology.org/GO.format.annotation.shtml
gp_association (GPA format) README:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gp_association_readme

gp_information (GPI format) README:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gp_information_readme
"""

import copy
import sys

from Bio._py3k import zip

# GAF: GO Annotation Format
#
# GAF version 2.0

GAF20FIELDS = ['DB',
        'DB_Object_ID',
        'DB_Object_Symbol',
        'Qualifier',
        'GO_ID',
        'DB:Reference',
        'Evidence',
        'With',
        'Aspect',
        'DB_Object_Name',
        'Synonym',
        'DB_Object_Type',
        'Taxon_ID',
        'Date',
        'Assigned_By',
        'Annotation_Extension',
        'Gene_Product_Form_ID']

# GAF version 1.0
GAF10FIELDS = ['DB',
        'DB_Object_ID',
        'DB_Object_Symbol',
        'Qualifier',
        'GO_ID',
        'DB:Reference',
        'Evidence',
        'With',
        'Aspect',
        'DB_Object_Name',
        'Synonym',
        'DB_Object_Type',
        'Taxon_ID',
        'Date',
        'Assigned_By']


# GPA version 1.0
GPA10FIELDS = [
      'DB',
      'DB_Object_ID',
      'Qualifier',
      'GO_ID',
      'DB:Reference',
      'Evidence code',
      'With',
      'Interacting_taxon_ID',
      'Date',
      'Assigned_by',
      'Annotation_Extension',
      'Spliceform_ID']

# GPA version 1.1
GPA11FIELDS = [
      'DB',
      'DB_Object_ID',
      'Qualifier',
      'GO_ID',
      'DB:Reference',
      'ECO_Evidence_code',
      'With',
      'Interacting_taxon_ID',
      'Date',
      'Assigned_by',
      'Annotation Extension',
      'Annotation_Properties']

# GPI version 1.0
GPI10FIELDS = [
      'DB',
      'DB_subset',
      'DB_Object_ID',
      'DB_Object_Symbol',
      'DB_Object_Name',
      'DB_Object_Synonym',
      'DB_Object_Type',
      'Taxon',
      'Annotation_Target_Set',
      'Annotation_Completed',
      'Parent_Object_ID']

# GPI version 1.1
GPI11FIELDS = [
      'DB_Object_ID',
      'DB_Object_Symbol',
      'DB_Object_Name',
      'DB_Object_Synonym',
      'DB_Object_Type',
      'Taxon',
      'Parent_Object_ID',
      'DB_Xref',
      'Gene_Product_Properties',
      'Annotation_Target_Set',
      'GO_Annotation_Complete']


def _gpi10iterator(handle):
    """Read GPI 1.0 format files (PRIVATE).

    This iterator is used to read a gp_information.goa_uniprot
    file which is in the GPI 1.0 format.
    """
    for inline in handle:
        if inline[0] == '!':
            continue
        inrec = inline.rstrip('\n').split('\t')
        if len(inrec) == 1:
            continue
        inrec[5] = inrec[5].split('|') # DB_Object_Synonym(s)
        inrec[8] = inrec[8].split('|') # Annotation_Target_Set
        yield dict(zip(GPI10FIELDS, inrec))


def _gpi11iterator(handle):
    """Read GPI 1.0 format files (PRIVATE).

    This iterator is used to read a gp_information.goa_uniprot
    file which is in the GPI 1.0 format.
    """
    for inline in handle:
        if inline[0] == '!':
            continue
        inrec = inline.rstrip('\n').split('\t')
        if len(inrec) == 1:
            continue
        inrec[2] = inrec[2].split('|') # DB_Object_Name
        inrec[3] = inrec[3].split('|') # DB_Object_Synonym(s)
        inrec[7] = inrec[7].split('|') # DB_Xref(s)
        inrec[8] = inrec[8].split('|') # Properties
        yield dict(zip(GPI11FIELDS, inrec))


def gpi_iterator(handle):
    """Read GPI format files.

    This function should be called to read a
    gp_information.goa_uniprot file. At the moment, there is
    only one format, but this may change, so
    this function is a placeholder a future wrapper.
    """
    inline = handle.readline()
    if inline.strip() == '!gpi-version: 1.1':
        sys.stderr.write("gpi 1.1\n")
        return _gpi11iterator(handle)
    else:
        sys.stderr.write("gpi 1.0\n")
        return _gpi10iterator(handle)


def _gpa10iterator(handle):
    """Read GPA 1.0 format files (PRIVATE).

    This iterator is used to read a gp_association.*
    file which is in the GPA 1.0 format. Do not call directly. Rather,
    use the gpaiterator function.
    """

    for inline in handle:
        if inline[0] == '!':
            continue
        inrec = inline.rstrip('\n').split('\t')
        if len(inrec) == 1:
            continue
        inrec[2] = inrec[2].split('|') # Qualifier
        inrec[4] = inrec[4].split('|') # DB:Reference(s)
        inrec[6] = inrec[6].split('|') # With
        inrec[10] = inrec[10].split('|') # Annotation extension
        yield dict(zip(GPA10FIELDS, inrec))


def _gpa11iterator(handle):
    """Read GPA 1.1 format files (PRIVATE).

    This iterator is used to read a gp_association.goa_uniprot
    file which is in the GPA 1.1 format. Do not call directly. Rather
    use the gpa_iterator function
    """
    for inline in handle:
        if inline[0] == '!':
            continue
        inrec = inline.rstrip('\n').split('\t')
        if len(inrec) == 1:
            continue
        inrec[2] = inrec[2].split('|') # Qualifier
        inrec[4] = inrec[4].split('|') # DB:Reference(s)
        inrec[6] = inrec[6].split('|') # With
        inrec[10] = inrec[10].split('|') # Annotation extension
        yield dict(zip(GPA11FIELDS, inrec))


def gpa_iterator(handle):
    """Wrapper function: read GPA format files.

    This function should be called to read a
    gene_association.goa_uniprot file. Reads the first record and
    returns a gpa 1.1 or a gpa 1.0 iterator as needed
    """
    inline = handle.readline()
    if inline.strip() == '!gpa-version: 1.1':
        sys.stderr.write("gpa 1.1\n")
        return _gpa11iterator(handle)
    else:
        sys.stderr.write("gpa 1.0\n")
        return _gpa10iterator(handle)


def _gaf20iterator(handle):
    for inline in handle:
        if inline[0] == '!':
            continue
        inrec = inline.rstrip('\n').split('\t')
        if len(inrec) == 1:
            continue
        inrec[3] = inrec[3].split('|')  # Qualifier
        inrec[5] = inrec[5].split('|')  # DB:reference(s)
        inrec[7] = inrec[7].split('|')  # With || From
        inrec[10] = inrec[10].split('|')  # Synonym
        inrec[12] = inrec[12].split('|')  # Taxon
        yield dict(zip(GAF20FIELDS, inrec))


def _gaf10iterator(handle):
    for inline in handle:
        if inline[0] == '!':
            continue
        inrec = inline.rstrip('\n').split('\t')
        if len(inrec) == 1:
            continue
        inrec[3] = inrec[3].split('|')  # Qualifier
        inrec[5] = inrec[5].split('|')  # DB:reference(s)
        inrec[7] = inrec[7].split('|')  # With || From
        inrec[10] = inrec[10].split('|')  # Synonym
        inrec[12] = inrec[12].split('|')  # Taxon
        yield dict(zip(GAF10FIELDS, inrec))


def _gaf10byproteiniterator(handle):
    cur_id = None
    id_rec_list = []
    for inline in handle:
        if inline[0] == '!':
            continue
        inrec = inline.rstrip('\n').split('\t')
        if len(inrec) == 1:
            continue
        inrec[3] = inrec[3].split('|')  # Qualifier
        inrec[5] = inrec[5].split('|')  # DB:reference(s)
        inrec[7] = inrec[7].split('|')  # With || From
        inrec[10] = inrec[10].split('|')  # Synonym
        inrec[12] = inrec[12].split('|')  # Taxon
        cur_rec = dict(zip(GAF10FIELDS, inrec))
        if cur_rec['DB_Object_ID'] != cur_id and cur_id:
            ret_list = copy.copy(id_rec_list)
            id_rec_list = [cur_rec]
            cur_id = cur_rec['DB_Object_ID']
            yield ret_list
        else:
            cur_id = cur_rec['DB_Object_ID']
            id_rec_list.append(cur_rec)


def _gaf20byproteiniterator(handle):
    cur_id = None
    id_rec_list = []
    for inline in handle:
        if inline[0] == '!':
            continue
        inrec = inline.rstrip('\n').split('\t')
        if len(inrec) == 1:
            continue
        inrec[3] = inrec[3].split('|')  # Qualifier
        inrec[5] = inrec[5].split('|')  # DB:reference(s)
        inrec[7] = inrec[7].split('|')  # With || From
        inrec[10] = inrec[10].split('|')  # Synonym
        inrec[12] = inrec[12].split('|')  # Taxon
        cur_rec = dict(zip(GAF20FIELDS, inrec))
        if cur_rec['DB_Object_ID'] != cur_id and cur_id:
            ret_list = copy.copy(id_rec_list)
            id_rec_list = [cur_rec]
            cur_id = cur_rec['DB_Object_ID']
            yield ret_list
        else:
            cur_id = cur_rec['DB_Object_ID']
            id_rec_list.append(cur_rec)


def gafbyproteiniterator(handle):
    """Iterates over records in a gene association file.

    Returns a list of all consecutive records with the same DB_Object_ID
    This function should be called to read a
    gene_association.goa_uniprot file. Reads the first record and
    returns a gaf 2.0 or a gaf 1.0 iterator as needed
    """
    inline = handle.readline()
    if inline.strip() == '!gaf-version: 2.0':
        sys.stderr.write("gaf 2.0\n")
        return _gaf20byproteiniterator(handle)
    else:
        sys.stderr.write("gaf 1.0\n")
        return _gaf10byproteiniterator(handle)


def gafiterator(handle):
    """Iterate pver a GAF 1.0 or 2.0 file.

    This function should be called to read a
    gene_association.goa_uniprot file. Reads the first record and
    returns a gaf 2.0 or a gaf 1.0 iterator as needed
    """
    inline = handle.readline()
    if inline.strip() == '!gaf-version: 2.0':
        sys.stderr.write("gaf 2.0\n")
        return _gaf20iterator(handle)
    else:
        sys.stderr.write("gaf 1.0\n")
        return _gaf10iterator(handle)


def writerec(outrec, handle, fields=GAF20FIELDS):
    """Write a single UniProt-GOA record to an output stream.

    Caller should know the  format version. Default: gaf-2.0
    If header has a value, then it is assumed this is the first record,
    a header is written.
    """
    outstr = ''
    for field in fields[:-1]:
        if isinstance(outrec[field], list):
            for subfield in outrec[field]:
                outstr += subfield + '|'
            outstr = outstr[:-1] + '\t'
        else:
            outstr += outrec[field] + '\t'
    outstr += outrec[fields[-1]] + '\n'
    handle.write("%s" % outstr)


def writebyproteinrec(outprotrec, handle, fields=GAF20FIELDS):
    """Write a list of GAF records to an output stream.

    Caller should know the  format version. Default: gaf-2.0
    If header has a value, then it is assumed this is the first record,
    a header is written. Typically the list is the one read by fafbyproteinrec, which
    contains all consecutive lines with the same DB_Object_ID
    """
    for outrec in outprotrec:
        writerec(outrec, handle, fields=fields)


def record_has(inrec, fieldvals):
    """Accepts a record, and a dictionary of field values.

    The format is {'field_name': set([val1, val2])}.
    If any field in the record has  a matching value, the function returns
    True. Otherwise, returns False.
    """
    retval = False
    for field in fieldvals:
        if isinstance(inrec[field], str):
            set1 = set([inrec[field]])
        else:
            set1 = set(inrec[field])
        if (set1 & fieldvals[field]):
            retval = True
            break
    return retval


if __name__ == '__main__':
    """Example: read and filter a GAF file.

    Write only S. cerevisiae records, but remove all
    records with IEA evidence
    """
    banned = {'Evidence': set(['IEA', 'EXP'])}
    allowed = {'Taxon_ID': set(['taxon:4932'])}
    for inrec in gafiterator(open(sys.argv[1])):
        if record_has(inrec, allowed) and \
               not record_has(inrec, banned):
            writerec(inrec, sys.stdout, GAF10FIELDS)
