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mvdbeekmvdbeek
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Merge pull request #1 from abretaud/bz2
Add fastq(*).bz2 datatypes and converters
2 parents 304c05f + 99a037d commit 833f2c3

16 files changed

Lines changed: 163 additions & 14 deletions

‎config/datatypes_conf.xml.sample‎

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@@ -99,6 +99,21 @@
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<datatype extension="fastqillumina.gz" type="galaxy.datatypes.sequence:FastqIlluminaGz" display_in_upload="true">
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<converter file="fastqilluminagz_to_fastqillumina.xml" target_datatype="fastqillumina"/>
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</datatype>
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<datatype extension="fastq.bz2" type="galaxy.datatypes.sequence:FastqBz2" display_in_upload="true">
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<converter file="fastqbz2_to_fastq.xml" target_datatype="fastq"/>
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</datatype>
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<datatype extension="fastqsanger.bz2" type="galaxy.datatypes.sequence:FastqSangerBz2" display_in_upload="true">
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<converter file="fastqsangerbz2_to_fastqsanger.xml" target_datatype="fastqsanger"/>
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</datatype>
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<datatype extension="fastqsolexa.bz2" type="galaxy.datatypes.sequence:FastqSolexaBz2" display_in_upload="true">
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<converter file="fastqsolexabz2_to_fastqsolexa.xml" target_datatype="fastqsolexa"/>
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</datatype>
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<datatype extension="fastqcssanger.bz2" type="galaxy.datatypes.sequence:FastqCSSangerBz2" display_in_upload="true">
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<converter file="fastqcssangerbz2_to_fastqcssanger.xml" target_datatype="fastqcssanger"/>
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</datatype>
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<datatype extension="fastqillumina.bz2" type="galaxy.datatypes.sequence:FastqIlluminaBz2" display_in_upload="true">
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<converter file="fastqilluminabz2_to_fastqillumina.xml" target_datatype="fastqillumina"/>
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</datatype>
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<datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
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<datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
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<datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/>
@@ -638,6 +653,7 @@
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<sniffer type="galaxy.datatypes.sequence:Fasta"/>
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<sniffer type="galaxy.datatypes.sequence:Fastq"/>
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<sniffer type="galaxy.datatypes.sequence:FastqGz"/>
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<sniffer type="galaxy.datatypes.sequence:FastqBz2"/>
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<sniffer type="galaxy.datatypes.interval:Wiggle"/>
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<sniffer type="galaxy.datatypes.text:Html"/>
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<sniffer type="galaxy.datatypes.images:Pdf"/>

‎lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml‎

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<tool id="CONVERTER_fastqbz2_to_fastq" name="Convert fastq.bz2 files to fastq" version="1.0.0" hidden="true">
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<command>bzip2 -dcf '$input1' > '$output1'</command>
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<inputs>
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<param format="fastq.bz2" name="input1" type="data" label="Choose FASTQ file"/>
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</inputs>
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<outputs>
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<data format="fastq" name="output1"/>
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</outputs>
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<help>
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</help>
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</tool>

‎lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml‎

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<tool id="CONVERTER_fastqcssangerbz2_to_fastqcssanger" name="Convert fastqcssanger.bz2 files to fastqcssanger" version="1.0.0" hidden="true">
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<command>bzip2 -dcf '$input1' > '$output1'</command>
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<inputs>
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<param format="fastqcssanger.bz2" name="input1" type="data" label="Choose FASTQ file"/>
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</inputs>
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<outputs>
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<data format="fastqcssanger" name="output1"/>
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</outputs>
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<help>
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</help>
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</tool>

‎lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml‎

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@@ -1,10 +1,8 @@
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<tool id="CONVERTER_fastqcssangergz_to_fastqcssanger" name="Convert fastqcssanger.gz files to fastqcssanger" version="1.0.0" hidden="true">
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<command>gzip -dcf '$input1' > '$output1'</command>
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<inputs>
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<page>
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<param format="fastqcssanger.gz" name="input1" type="data" label="Choose FASTQ file"/>
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</page>
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</inputs>
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<param format="fastqcssanger.gz" name="input1" type="data" label="Choose FASTQ file"/>
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</inputs>
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<outputs>
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<data format="fastqcssanger" name="output1"/>
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</outputs>

‎lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml‎

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<tool id="CONVERTER_fastqilluminabz2_to_fastqillumina" name="Convert fastqillumina.bz2 files to fastqillumina" version="1.0.0" hidden="true">
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<command>bzip2 -dcf '$input1' > '$output1'</command>
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<inputs>
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<param format="fastqillumina.bz2" name="input1" type="data" label="Choose FASTQ file"/>
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</inputs>
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<outputs>
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<data format="fastqillumina" name="output1"/>
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</outputs>
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<help>
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</help>
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</tool>

‎lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml‎

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<command>gzip -dcf '$input1' > '$output1'</command>
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<inputs>
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<param format="fastqillumina.gz" name="input1" type="data" label="Choose FASTQ file"/>
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</inputs>
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</inputs>
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<outputs>
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<data format="fastqillumina" name="output1"/>
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</outputs>

‎lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml‎

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<tool id="CONVERTER_fastqsangerbz2_to_fastqsanger" name="Convert fastqsanger.bz2 files to fastqsanger" version="1.0.0" hidden="true">
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<command>bzip2 -dcf '$input1' > '$output1'</command>
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<inputs>
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<param format="fastqsanger.bz2" name="input1" type="data" label="Choose FASTQ file"/>
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</inputs>
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<outputs>
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<data format="fastqsanger" name="output1"/>
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</outputs>
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<help>
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</help>
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</tool>

‎lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml‎

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<tool id="CONVERTER_fastqsolexabz2_to_fastqsolexa" name="Convert fastqsolexa.bz2 files to fastqsolexa" version="1.0.0" hidden="true">
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<command>bzip2 -dcf '$input1' > '$output1'</command>
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<inputs>
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<param format="fastqsolexa.bz2" name="input1" type="data" label="Choose FASTQ file"/>
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</inputs>
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<outputs>
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<data format="fastqsolexa" name="output1"/>
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</outputs>
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<help>
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</help>
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</tool>

‎lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml‎

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@@ -2,7 +2,7 @@
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<command>gzip -dcf '$input1' > '$output1'</command>
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<inputs>
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<param format="fastqsolexa.gz" name="input1" type="data" label="Choose FASTQ file"/>
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</inputs>
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</inputs>
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<outputs>
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<data format="fastqsolexa" name="output1"/>
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</outputs>

‎lib/galaxy/datatypes/sequence.py‎

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@@ -3,6 +3,7 @@
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"""
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import gzip
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import bz2
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import json
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import logging
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import os
@@ -572,10 +573,13 @@ def set_meta( self, dataset, **kwd ):
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data_lines = 0
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sequences = 0
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seq_counter = 0 # blocks should be 4 lines long
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compressed = is_gzip(dataset.file_name)
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compressed_gzip = is_gzip(dataset.file_name)
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compressed_bzip2 = is_bz2(dataset.file_name)
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try:
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if compressed:
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if compressed_gzip:
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in_file = gzip.GzipFile(dataset.file_name)
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elif compressed_bzip2:
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in_file = bz2.BZ2File(dataset.file_name)
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else:
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in_file = open(dataset.file_name)
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for line in in_file:
@@ -615,7 +619,7 @@ def sniff( self, filename ):
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>>> Fastq().sniff( fname )
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True
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"""
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compressed = is_gzip(filename)
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compressed = is_gzip(filename) or is_bz2(filename)
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if compressed and not isinstance(self, Binary):
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return False
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headers = get_headers( filename, None )
@@ -743,6 +747,40 @@ class FastqCSSangerGz( FastqGz ):
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Binary.register_sniffable_binary_format("fastqcssanger.gz", "fastqcssanger.gz", FastqCSSangerGz)
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class FastqBz2 ( BaseFastq, Binary ):
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"""Class representing a generic compressed FASTQ sequence"""
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edam_format = "format_1930"
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file_ext = "fastq.gz"
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Binary.register_sniffable_binary_format("fastq.gz", "fastq.gz", FastqGz)
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class FastqSangerBz2( FastqBz2 ):
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"""Class representing a compressed FASTQ sequence ( the Sanger variant )"""
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edam_format = "format_1932"
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file_ext = "fastqsanger.bz2"
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Binary.register_sniffable_binary_format("fastqsanger.bz2", "fastqsanger.bz2", FastqSangerBz2)
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class FastqSolexaBz2( FastqBz2 ):
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"""Class representing a compressed FASTQ sequence ( the Solexa variant )"""
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edam_format = "format_1933"
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file_ext = "fastqsolexa.bz2"
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Binary.register_sniffable_binary_format("fastqsolexa.bz2", "fastqsolexa.bz2", FastqSolexaBz2)
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class FastqIlluminaBz2( FastqBz2 ):
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"""Class representing a compressed FASTQ sequence ( the Illumina 1.3+ variant )"""
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edam_format = "format_1931"
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file_ext = "fastqillumina.bz2"
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Binary.register_sniffable_binary_format("fastqillumina.bz2", "fastqillumina.bz2", FastqIlluminaBz2)
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class FastqCSSangerBz2( FastqBz2 ):
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"""Class representing a Color Space compressed FASTQ sequence ( e.g a SOLiD variant )"""
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file_ext = "fastqcssanger.bz2"
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Binary.register_sniffable_binary_format("fastqcssanger.bz2", "fastqcssanger.bz2", FastqCSSangerBz2)
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class Maf( Alignment ):
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"""Class describing a Maf alignment"""
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edam_format = "format_3008"

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