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This commit is contained in:
Anton Nekrutenko
2009-09-21 10:32:48 -04:00
parent 2cd2c865ad
commit 8d0e39c9f8
5 changed files with 59 additions and 56 deletions
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tool_conf.xml.sample
+22 -23
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@@ -169,29 +169,28 @@
<tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
<tool file="fastx_toolkit/fastx_collapser.xml" />
</section>
<section name="NGS: FASTQ QC and manipulation" id="cshl_library_information">
<tool file="fastx_toolkit/fastx_quality_statistics.xml" />
<tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
<tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
<!-- <tool file="fastx_toolkit/fasta_clipping_histogram.xml" /> -->
<tool file="fastx_toolkit/fastq_to_fasta.xml" />
<tool file="fastx_toolkit/fastq_quality_converter.xml" />
<!-- <tool file="fastx_toolkit/fastx_clipper.xml" /> -->
<tool file="fastx_toolkit/fastx_trimmer.xml" />
<tool file="fastx_toolkit/fastx_renamer.xml" />
<tool file="fastx_toolkit/fastx_reverse_complement.xml" />
<tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
<tool file="fastx_toolkit/fastq_quality_filter.xml" />
<!--<tool file="fastx_toolkit/fastx_barcode_splitter.xml" />-->
<tool file="metag_tools/split_paired_reads.xml" />
</section>
<section name="454: QC" id="short_read_analysis">
<tool file="metag_tools/short_reads_figure_score.xml" />
<tool file="metag_tools/short_reads_trim_seq.xml" />
</section>
<section name="SOLiD: QC" id="solid_tools">
<tool file="solid_tools/solid_qual_stats.xml" />
<tool file="solid_tools/solid_qual_boxplot.xml" />
<section name="NGS: QC and manipulation" id="cshl_library_information">
<label text="Genetic FASTQ data" id="fastq" />
<tool file="fastx_toolkit/fastx_quality_statistics.xml" />
<tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
<tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
<!-- <tool file="fastx_toolkit/fasta_clipping_histogram.xml" /> -->
<tool file="fastx_toolkit/fastq_to_fasta.xml" />
<tool file="fastx_toolkit/fastq_quality_converter.xml" />
<!-- <tool file="fastx_toolkit/fastx_clipper.xml" /> -->
<tool file="fastx_toolkit/fastx_trimmer.xml" />
<tool file="fastx_toolkit/fastx_renamer.xml" />
<tool file="fastx_toolkit/fastx_reverse_complement.xml" />
<tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
<tool file="fastx_toolkit/fastq_quality_filter.xml" />
<!--<tool file="fastx_toolkit/fastx_barcode_splitter.xml" />-->
<tool file="metag_tools/split_paired_reads.xml" />
<label text="Roche-454 Specific" id="454" />
<tool file="metag_tools/short_reads_figure_score.xml" />
<tool file="metag_tools/short_reads_trim_seq.xml" />
<label text="AB-SOLiD Specific" id="solid" />
<tool file="solid_tools/solid_qual_stats.xml" />
<tool file="solid_tools/solid_qual_boxplot.xml" />
</section>
<section name="NGS: Mapping" id="solexa_tools">
<!-- <tool file="sr_mapping/lastz_wrapper.xml" /> -->
tools/samtools/pileup_parser.pl
+9 -8
View File
@@ -1,6 +1,8 @@
#! /usr/bin/perl -w
use strict;
use POSIX;
die "Usage: pileup_parser.pl <in_file> <ref_base_column> <read_bases_column> <base_quality_column> <coverage column> <qv cutoff> <coverage cutoff> <SNPs only?> <output bed?> <coord_column> <out_file>\n" unless @ARGV == 11;
@@ -28,10 +30,12 @@ open (OUT, ">$out_file") or die "Cannot open $out_file $!\n";
while (<IN>) {
chop;
next if m/^\#/;
my @fields = split /\t/;
next if $fields[ $ref_base_column ] eq "*"; # skip indel lines
next if $fields[ $cvrg_column ] < $cvrg_cutoff; # skip low coverage lines
my $read_bases = $fields[ $read_bases_column ];
my $read_bases = $fields[ $read_bases_column ];
die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not isdigit $fields[ $cvrg_column ] );
next if $fields[ $cvrg_column ] < $cvrg_cutoff;
my $base_quality = $fields[ $base_quality_column ];
if ($read_bases =~ m/[\$\^\+-]/) {
@@ -42,11 +46,8 @@ while (<IN>) {
$read_bases =~ s/[\+-]{1}$indel_len.{$indel_len}//; # remove indel info from read base field
}
}
if ( length($read_bases) != length($base_quality) ) {
$first_skipped_line = $_ if $invalid_line_counter == 0;
++$invalid_line_counter;
}
die "Error parsing read bases and qualities in line $.. Last processed line conatined these values: " . join("\t", @fields) . "\n" if ( length($read_bases) != length($base_quality) );
# after removing read block and indel data the length of read_base
# field should identical to the length of base_quality field
@@ -95,4 +96,4 @@ while (<IN>) {
print STDERR "Could not parse $invalid_line_counter line(s) beginning with: $first_skipped_line\n" if $invalid_line_counter > 0;
close IN;
close OUT;
close OUT;
tools/samtools/sam2interval.py
+1 -1
View File
@@ -78,7 +78,7 @@ options (listed below) default to 'None' if omitted
for line in infile:
line = line.rstrip( '\r\n' )
if line and not line.startswith( '#,@' ):
if line and not line.startswith( '#' ) and not line.startswith( '@' ) :
fields = line.split( '\t' )
start = int( fields[ int( options.start_col ) - 1 ] ) - 1
end = 0
tools/samtools/sam_bitwise_flag_filter.py
+1 -1
View File
@@ -135,7 +135,7 @@ options (listed below) default to 'None' if omitted
for line in infile:
line = line.rstrip( '\r\n' )
if line and not line.startswith( '#' ):
if line and not line.startswith( '#' ) and not line.startswith( '@' ) :
fields = line.split( '\t' )
sam_states = []
sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0001 ) )
tools/sr_mapping/bowtie_wrapper.xml
+26 -23
View File
@@ -336,7 +336,7 @@
</param>
</when>
</conditional>
<param name="offrate" type="integer" value="-1" label="Override the offrate of the index to n -o)" help="-1 for default" />
<param name="offrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
<param name="seed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
</when> <!-- full -->
</conditional> <!-- params -->
@@ -443,31 +443,34 @@ Bowtie accepts files in Sanger FASTQ format.
The output is in SAM format, and has the following columns::
1 QNAME - Query (pair) NAME
2 FLAG - bitwise FLAG
3 RNAME - Reference sequence NAME
4 POS - 1-based leftmost POSition/coordinate of clipped sequence
5 MAPQ - MAPping Quality (Phred-scaled)
6 CIGAR - extended CIGAR string
7 MRNM - Mate Reference sequence NaMe ('=' if same as RNAME)
8 MPOS - 1-based Mate POSition
9 ISIZE - Inferred insert SIZE
10 SEQ - query SEQuence on the same strand as the reference
11 QUAL - query QUALity (ASCII-33 gives the Phred base quality)
12 OPT - variable OPTional fields in the format TAG:VTYPE:VALU
Column Description
-------- --------------------------------------------------------
1 QNAME Query (pair) NAME
2 FLAG bitwise FLAG
3 RNAME Reference sequence NAME
4 POS 1-based leftmost POSition/coordinate of clipped sequence
5 MAPQ MAPping Quality (Phred-scaled)
6 CIGAR extended CIGAR string
7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
8 MPOS 1-based Mate POSition
9 ISIZE Inferred insert SIZE
10 SEQ query SEQuence on the same strand as the reference
11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
The flags are as follows::
Flag - Description
0x0001 - the read is paired in sequencing
0x0002 - the read is mapped in a proper pair
0x0004 - the query sequence itself is unmapped
0x0008 - the mate is unmapped
0x0010 - strand of the query (1 for reverse)
0x0020 - strand of the mate
0x0040 - the read is the first read in a pair
0x0080 - the read is the second read in a pair
0x0100 - the alignment is not primary
Flag Description
------ -------------------------------------
0x0001 the read is paired in sequencing
0x0002 the read is mapped in a proper pair
0x0004 the query sequence itself is unmapped
0x0008 the mate is unmapped
0x0010 strand of the query (1 for reverse)
0x0020 strand of the mate
0x0040 the read is the first read in a pair
0x0080 the read is the second read in a pair
0x0100 the alignment is not primary
It looks like this (scroll sideways to see the entire example)::