"""

@return: the body of a form

"""

# define the list of form objects

form_objects = [

Form.SingleLine('chromosome', 'chromosome', 'chr17'),

Form.Integer('position', 'position', 70360012, low=0),

Form.RadioGroup('output', 'output options', [

RadioItem('show_alignment', 'show the aligned region', True),

RadioItem('show_column', 'show the aligned column')])]

try:

finder = KGEA.Finder(

g_index_dir, g_valid_chromosome_strings_pathname, g_fasta_dir)

if fs.show_alignment:

lines = finder.get_alignment_lines(fs.chromosome, fs.position)

elif fs.show_column:

lines = finder.get_column_lines(fs.chromosome, fs.position)

if lines:

return '\n'.join(lines) + '\n'

else:

msg = 'this position has no corresponding amino acid'

raise KGEA.KGEAError(msg)

except KGEA.KGEAError as e:

"""

@param options: from optparse

@param args: from optparse

@return: a response string

"""

# get this file from the web directory

# http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way/alignments/

original_fasta_filename = 'knownGene.exonAA.fa'

# the original fasta file is broken into a bunch of pieces and put into this directory

pieces_directory = 'fasta'

# the index files that map genomic locations to fasta subfiles are in this directory

index_directory = 'index'

# this file keeps a list of valid chromosome names from the original fasta file

chromosome_filename = 'chromosomes.txt'

# assert that a command was given with the script

if not args:

raise MySyntaxError('no command was given')

# try to dispatch the command

command = args[0]

command_args = args[1:]

if command == 'split':

if command_args:

raise MySyntaxError('the split command does not take any arguments')

# assert that the fasta directory has been created

if not os.path.isdir(pieces_directory):

err_lines = [

'The directory for the split fasta files was not found: ' + pieces_directory,

'Please create this directory or cd to its parent directory.']

raise MyConfigError('\n'.join(err_lines))

# assert that the current directory has the original huge fasta file

pathnames = os.listdir('.')

if original_fasta_filename not in pathnames:

err_lines = [

'The file %s was not found in the current directory.' % original_fasta_filename,

'Please download this file from:',

'http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way/alignments/']

raise MyConfigError('\n'.join(err_lines))

splitter = KGEA.Splitter(original_fasta_filename, pieces_directory)

splitter.run(verbose=options.verbose)

return ''

elif command == 'index':

if command_args:

raise MySyntaxError('the index command does not take any arguments')

# assert that the fasta directory has been created

if not os.path.isdir(pieces_directory):

err_lines = [

'The directory for the split fasta files was not found: ' + pieces_directory,

'If this directory exists somewhere else, then cd to its parent directory.',

'If this directory has not been created, then create it and run the split command.']

raise MyConfigError('\n'.join(err_lines))

# assert that the index directory has been created

if not os.path.isdir(index_directory):

err_lines = [

'The directory for the index files was not found: ' + index_directory,

'Please create this directory or cd to its parent directory.']

raise MyConfigError('\n'.join(err_lines))

indexer = KGEA.Indexer(index_directory, chromosome_filename, pieces_directory)

indexer.run(verbose=options.verbose)

return ''

elif command == 'find-alignment':

if len(command_args) != 2:

raise MySyntaxError('the find-alignment command takes two arguments')

# define the chromosome string and the chromosome position

chromosome_string, chromosome_position_string = command_args

# initialize the chromosome position and assert that it is plausible

try:

chromosome_position = int(chromosome_position_string)

except ValueError as e:

raise MySyntaxError('the chromosome position should be an integer')

# assert that the fasta directory has been created

if not os.path.isdir(pieces_directory):

err_lines = [

'The directory for the split fasta files was not found: ' + pieces_directory,

'If this directory exists somewhere else, then cd to its parent directory.',

'If this directory has not been created, then create it and run the split command.']

raise MyConfigError('\n'.join(err_lines))

# assert that the index directory has been created

if not os.path.isdir(index_directory):

err_lines = [

'The directory for the index files was not found: ' + index_directory,

'If this directory exists somewhere else, then cd to its parent directory.',

'If this directory has not been created, then create it and run the index command.']

raise MyConfigError('\n'.join(err_lines))

# look for the alignment using the finder

finder = KGEA.Finder(index_directory, chromosome_filename, pieces_directory)

fasta_lines = finder.get_alignment_lines(chromosome_string, chromosome_position, verbose=options.verbose)

if not fasta_lines:

return 'no amino acid was found at this position'

return '\n'.join(fasta_lines)

elif command == 'find-column':

if len(command_args) != 2:

raise MySyntaxError('the find-column command takes two arguments')

# define the chromosome string and the chromosome position

chromosome_string, chromosome_position_string = command_args

# initialize the chromosome position and assert that it is plausible

try:

chromosome_position = int(chromosome_position_string)

except ValueError as e:

raise MySyntaxError('the chromosome position should be an integer')

# assert that the fasta directory has been created

if not os.path.isdir(pieces_directory):

err_lines = [

'The directory for the split fasta files was not found: ' + pieces_directory,

'If this directory exists somewhere else, then cd to its parent directory.',

'If this directory has not been created, then create it and run the split command.']

raise MyConfigError('\n'.join(err_lines))

# assert that the index directory has been created

if not os.path.isdir(index_directory):

err_lines = [

'The directory for the index files was not found: ' + index_directory,

'If this directory exists somewhere else, then cd to its parent directory.',

'If this directory has not been created, then create it and run the index command.']

raise MyConfigError('\n'.join(err_lines))

# look for the column using the finder

finder = KGEA.Finder(index_directory, chromosome_filename, pieces_directory)

column_lines = finder.get_column_lines(chromosome_string, chromosome_position, verbose=options.verbose)

if not column_lines:

return 'no amino acid was found at this position'

return '\n'.join(column_lines)

elif command == 'summarize':

if command_args:

raise MySyntaxError('the summarize command does not take any arguments')

# assert that the current directory has the original huge fasta file

pathnames = os.listdir('.')

if original_fasta_filename not in pathnames:

err_lines = [

'The file %s was not found in the current directory.' % original_fasta_filename,

'Please download this file from:',

'http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way/alignments/']

raise MyConfigError('\n'.join(err_lines))

# initialize the progress bar

nbytes_total = os.path.getsize(original_fasta_filename)

pbar = Progress.Bar(nbytes_total)

# initialize the summary

mod3 = {0:0, 1:0, 2:0}

length_diff_dict = {}

# summarize by reading each alignment from the file

approx_nbytes_read = 0

fin = open(original_fasta_filename)

for lines in Util.gen_paragraphs(fin):

# process the lines

header_line = lines[0]

p = KGEA.LocationParser(header_line)

genomic_length = (p.last_index - p.first_index) + 1

mod3[genomic_length % 3] += 1

diff = 3*p.length - genomic_length

if diff not in length_diff_dict:

length_diff_dict[diff] = 0

length_diff_dict[diff] += 1

# update the progress bar

approx_nbytes_read += sum(len(line) for line in lines)

pbar.update(approx_nbytes_read)

fin.close()

# finish the progress bar

pbar.update(nbytes_total)

# return the summary

summary_lines = []

summary_lines += ['genomic span of %d mod 3: %d sequences' % (i, mod3[i]) for i in range(3)]

summary_lines.append('histogram of 3*aa_length - genomic span:')

for key, value in sorted(length_diff_dict.items()):

summary_lines.append('%d : %d' % (key, value))

return '\n'.join(summary_lines)

else: