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add fastq converters to implicit data type converter.
This commit is contained in:
Wen-Yu Chung
@@ -2,6 +2,8 @@
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<converters>
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<converter file="bed_to_gff_converter.xml" source_datatype="bed" target_datatype="gff"/>
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<converter file="fasta_to_tabular_converter.xml" source_datatype="fasta" target_datatype="tabular"/>
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<converter file="fastq_to_fasta_converter.xml" source_datatype="fastq" target_datatype="fasta"/>
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<converter file="fastq_to_qual_converter.xml" source_datatype="fastq" target_datatype="qual"/>
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<converter file="gff_to_bed_converter.xml" source_datatype="gff" target_datatype="bed"/>
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<converter file="interval_to_bed_converter.xml" source_datatype="interval" target_datatype="bed"/>
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<converter file="maf_to_fasta_converter.xml" source_datatype="maf" target_datatype="fasta"/>
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@@ -0,0 +1,69 @@
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#! /usr/bin/python
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"""
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convert fastq file to separated sequence and quality files.
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assume each sequence and quality score are contained in one line
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the order should be:
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1st line: @title_of_seq
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2nd line: nucleotides
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3rd line: +title_of_qualityscore (might be skipped)
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4th line: quality scores
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(in three forms: a. digits, b. ASCII codes, the first char as the coding base, c. ASCII codes without the first char.)
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Usage:
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%python convert_fastq2fasta.py <your_fastq_filename> <output_seq_filename> <output_score_filename>
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"""
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import sys, os
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from math import *
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( "%s\n" % msg )
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sys.exit()
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if __name__ == '__main__':
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# file I/O
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infile = sys.argv[1]
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outfile_seq = open(sys.argv[2], 'w')
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# guessing the first char used in title lines
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leading_char_seq_title = ''
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every_four_lines = 0
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for i, line in enumerate(file(infile)):
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line = line.rstrip() # get rid of the newline and spaces
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if ((not line) or (line.startswith('#'))): continue # comments
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every_four_lines = (every_four_lines + 1) % 4
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leading_char = line[0:1]
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if every_four_lines == 1: # first line is expected to be read title
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if not leading_char_seq_title:
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leading_char_seq_title = leading_char
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if leading_char != leading_char_seq_title:
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stop_err('Invalid fastq format at line %d.' %(i))
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read_title = line[1:]
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outfile_seq.write('>%s\n' %(line[1:]))
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elif every_four_lines == 2: # second line is expected to be read
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read_length = len(line)
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outfile_seq.write('%s\n' %(line))
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else:
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pass
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outfile_seq.close()
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@@ -0,0 +1,12 @@
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<tool id="CONVERTER_fastq_to_fasta_0" name="FASTQ-to-FASTA" version="1.0.0">
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<description>converts FASTQ file to FASTA format</description>
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<command interpreter="python">fastq_to_fasta_converter.py $input $output</command>
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<inputs>
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<param name="input" type="data" format="fastq" label="Fastq file"/>
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</inputs>
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<outputs>
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<data name="output" format="fasta"/>
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</outputs>
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<help>
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</help>
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</tool>
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@@ -0,0 +1,106 @@
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#! /usr/bin/python
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"""
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convert fastq file to separated sequence and quality files.
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assume each sequence and quality score are contained in one line
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the order should be:
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1st line: @title_of_seq
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2nd line: nucleotides
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3rd line: +title_of_qualityscore (might be skipped)
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4th line: quality scores
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(in three forms: a. digits, b. ASCII codes, the first char as the coding base, c. ASCII codes without the first char.)
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Usage:
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%python convert_fastq2fasta.py <your_fastq_filename> <output_seq_filename> <output_score_filename>
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"""
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import sys, os
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from math import *
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( "%s\n" % msg )
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sys.exit()
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if __name__ == '__main__':
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# file I/O
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infile = sys.argv[1]
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outfile_score = open(sys.argv[2], 'w')
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# guessing the first char used in title lines
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leading_char_quality_title = ''
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leading_char_seq_title = ''
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default_coding_value = 64
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every_four_lines = 0
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for i, line in enumerate(file(infile)):
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line = line.rstrip() # get rid of the newline and spaces
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if ((not line) or (line.startswith('#'))): continue # comments
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every_four_lines = (every_four_lines + 1) % 4
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leading_char = line[0:1]
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if every_four_lines == 1: # first line is expected to be read title
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if not leading_char_seq_title:
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leading_char_seq_title = leading_char
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if leading_char != leading_char_seq_title:
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stop_err('Invalid fastq format at line %d.' %(i))
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read_title = line[1:]
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elif every_four_lines == 2: # second line is expected to be read
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read_length = len(line)
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elif every_four_lines == 3: # third line is expected to be quality title
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if not leading_char_quality_title:
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leading_char_quality_title = leading_char
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if leading_char != leading_char_quality_title:
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stop_err('Invalid fastq format at line %d.' %(i))
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quality_title = line[1:]
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if (quality_title and (read_title != quality_title)):
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stop_err('Invalid fastq format: titles for sequence and quality score are different.')
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if not quality_title:
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outfile_score.write('>%s\n' %(read_title))
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else:
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outfile_score.write('>%s\n' %(line[1:]))
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else: # fourth line is expected to be the ASCII-coded quality scores
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qual = ''
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# peek: ascii code or digits?
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first_value = line.split()[0]
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if first_value.isdigit():
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# digits
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qual = line
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else:
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# ascii code
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# guess leading char
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quality_score_length = len(line)
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if quality_score_length == (read_length+1): # first char is leading_char_score
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leading_char_score = ord(line[0:1])
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line = line[1:]
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elif quality_score_length == read_length:
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leading_char_score = default_coding_value # default
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else:
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stop_err('Invalid fastq format: the number of quality scores is not the same as bases.')
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for j, char in enumerate(line):
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score = ord(char)-leading_char_score # 64
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qual += (str(score) + ' ')
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outfile_score.write('%s\n' %(qual))
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outfile_score.close()
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@@ -0,0 +1,11 @@
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<tool id="CONVERTER_fastq_to_qual_0" name="FASTQ-to-FASTA">
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<command interpreter="python">fastq_to_qual_converter.py $input1 $output1 </command>
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<inputs>
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<param format="fastq" name="input1" type="data" label="Fastq file"/>
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</inputs>
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<outputs>
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<data format="qual" name="output1" />
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</outputs>
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<help>
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</help>
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</tool>
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