From 32b3e24a97464ece773fdb99eb0813936aa4c348 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 17 Jul 2008 02:55:19 +0000 Subject: [PATCH] cleaning bp_usage git-svn-id: http://biopieces.googlecode.com/svn/trunk@162 74ccb610-7750-0410-82ae-013aeee3265d --- bp_usage/max_vals | 19 -------------- bp_usage/mean_vals | 22 ---------------- bp_usage/median_vals | 22 ---------------- bp_usage/merge_vals | 19 -------------- bp_usage/min_vals | 19 -------------- bp_usage/oligo_freq | 20 --------------- bp_usage/patscan_seq | 24 ------------------ bp_usage/plot_chrdist | 23 ----------------- bp_usage/plot_histogram | 26 ------------------- bp_usage/plot_karyogram | 21 ---------------- bp_usage/plot_lendist | 24 ------------------ bp_usage/plot_matches | 24 ------------------ bp_usage/plot_phastcons_profiles | 29 --------------------- bp_usage/plot_seqlogo | 18 ------------- bp_usage/random_records | 18 ------------- bp_usage/read_2bit | 26 ------------------- bp_usage/read_align | 29 --------------------- bp_usage/read_blast_tab | 33 ------------------------ bp_usage/read_embl | 24 ------------------ bp_usage/read_gff | 31 ----------------------- bp_usage/read_mysql | 23 ----------------- bp_usage/read_phastcons | 38 ---------------------------- bp_usage/read_psl | 43 -------------------------------- 23 files changed, 575 deletions(-) delete mode 100644 bp_usage/max_vals delete mode 100644 bp_usage/mean_vals delete mode 100644 bp_usage/median_vals delete mode 100644 bp_usage/merge_vals delete mode 100644 bp_usage/min_vals delete mode 100644 bp_usage/oligo_freq delete mode 100644 bp_usage/patscan_seq delete mode 100644 bp_usage/plot_chrdist delete mode 100644 bp_usage/plot_histogram delete mode 100644 bp_usage/plot_karyogram delete mode 100644 bp_usage/plot_lendist delete mode 100644 bp_usage/plot_matches delete mode 100644 bp_usage/plot_phastcons_profiles delete mode 100644 bp_usage/plot_seqlogo delete mode 100644 bp_usage/random_records delete mode 100644 bp_usage/read_2bit delete mode 100644 bp_usage/read_align delete mode 100644 bp_usage/read_blast_tab delete mode 100644 bp_usage/read_embl delete mode 100644 bp_usage/read_gff delete mode 100644 bp_usage/read_mysql delete mode 100644 bp_usage/read_phastcons delete mode 100644 bp_usage/read_psl diff --git a/bp_usage/max_vals b/bp_usage/max_vals deleted file mode 100644 index 5404948..0000000 --- a/bp_usage/max_vals +++ /dev/null @@ -1,19 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: February 2008 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Find the maximum value in the stream for given keys. - -Usage: ... | $script [options] - -Options: [-k | --keys=] - Comma separated list of keys to inspect. -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: ... | $script -k SEQ_LEN - Find the maximum SEQ_LEN. - -Keys out: _MAX - Maximum value of . diff --git a/bp_usage/mean_vals b/bp_usage/mean_vals deleted file mode 100644 index e078caa..0000000 --- a/bp_usage/mean_vals +++ /dev/null @@ -1,22 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Calculate the mean of values of given keys. - -Usage: ... | $script [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-k | --keys=] - Comma separated list of keys. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | $script -x -k SEQ_LEN,HIT_LEN -o result.txt - Calculate mean values and save to 'result.txt'. - -Keys out: _MEAN - Mean value of . - diff --git a/bp_usage/median_vals b/bp_usage/median_vals deleted file mode 100644 index 09de6a3..0000000 --- a/bp_usage/median_vals +++ /dev/null @@ -1,22 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: March 2008 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Calculate the median values of given keys. - -Usage: ... | $script [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-k | --keys=] - Comma separated list of keys. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | $script -x -k SEQ_LEN,HIT_LEN -o result.txt - Calculate median values and save to 'result.txt'. - -Keys out: _MEDIAN - Median value of . - diff --git a/bp_usage/merge_vals b/bp_usage/merge_vals deleted file mode 100644 index a2ced3f..0000000 --- a/bp_usage/merge_vals +++ /dev/null @@ -1,19 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Merge values of keys in a record so that all values are joined with a delimiter and saved as value of the first key. - -Usage: ... | $script [options] - -Options: [-k | --keys=] - List of values to merge. -Options: [-d | --delimit=] - Merge delimiter - Default='_' -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | $script -k SEQ_NAME,CHR,CHR_BEG,CHR_END - Merges specified values and saves in SEQ_NAME. - diff --git a/bp_usage/min_vals b/bp_usage/min_vals deleted file mode 100644 index 0838d43..0000000 --- a/bp_usage/min_vals +++ /dev/null @@ -1,19 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: February 2008 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Find the minimum value in the stream for given keys. - -Usage: ... | $script [options] - -Options: [-k | --keys=] - Comma separated list of keys to inspect. -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: ... | $script -k SEQ_LEN - Find the minimum SEQ_LEN. - -Keys out: _MIN - Minimum value of . diff --git a/bp_usage/oligo_freq b/bp_usage/oligo_freq deleted file mode 100644 index 6023d8a..0000000 --- a/bp_usage/oligo_freq +++ /dev/null @@ -1,20 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Determines the total oligo frequencies of sequences in stream. - -Usage: ... | oligo_freq [options] - -Options: [-w | --word_size=] - Size of oligos - Default=7. -Options: [-a | --all] - Accumulate oligos for all sequences in stream. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | oligo_freq -w 5 - Determines oligo frequency for all sequences in stream. -Examples: ... | oligo_freq -w 5 -a - Determines accumulated oligo frequency for all sequences in stream. - diff --git a/bp_usage/patscan_seq b/bp_usage/patscan_seq deleted file mode 100644 index 0d8d6ff..0000000 --- a/bp_usage/patscan_seq +++ /dev/null @@ -1,24 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Scan sequences in stream or genomes for patterns using scan_for_matches. - -Usage: ... | $script [options] -Usage: $script [options] -g - -Options: [-p | --patterns=] - Comma separated list of patterns to scan for. -Options: [-P | --patterns_in=] - File with one pattern per line. -Options: [-c | --comp] - Scan complementary strand as well. -Options: [-h | --max_hits=] - Stop scanning after max hits. -Options: [-m | --max_misses=] - Stop scanning after max misses. -Options: [-g | --genome= - Scan genome for pattern(s).] -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | $script -p AATTAA,ATTTAA - Scan sequences in stream for given patterns. -Examples: $script -g hg18 -P file.pat - Scan hg18 for patterns in 'file.pat'. diff --git a/bp_usage/plot_chrdist b/bp_usage/plot_chrdist deleted file mode 100644 index 7b803c3..0000000 --- a/bp_usage/plot_chrdist +++ /dev/null @@ -1,23 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Plot chromosome distribution of hits from e.g. BLAT or Vmatch. - -Usage: ... | plot_chrdist [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-t | --terminal=] - Terminal for output: dumb|post|svg - Default=dumb -Options: [-T | --title=] - Set plot title. -Options: [-X | --xlabel=] - Set x-axis label. -Options: [-Y | --ylabel=] - Set y-axis label. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | plot_chrdist -x - Create plot and output to STDOUT in ASCII. -Examples: ... | plot_chrdist -x -t svg -o plot.svg - Create plot and save to 'plot.svg'. diff --git a/bp_usage/plot_histogram b/bp_usage/plot_histogram deleted file mode 100644 index f763fc6..0000000 --- a/bp_usage/plot_histogram +++ /dev/null @@ -1,26 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: September 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Plot generic histogram. - -Usage: ... | plot_histogram [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-k | --key=] - Key to use for plotting. -Options: [-t | --terminal=] - Terminal for output: dumb|post|svg - Default=dumb -Options: [-T | --title=] - Set plot title. -Options: [-X | --xlabel=] - Set x-axis label. -Options: [-Y | --ylabel=] - Set y-axis label. -Options: [-s | --sort=] - Sort criteria for x-axis keys - Default=num -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | plot_histogram -x -k TISSUE - Create plot and output to STDOUT in ASCII. -Examples: ... | plot_histogram -x -k TISSUE -t svg -o plot.svg - Create plot and save to 'plot.svg'. - diff --git a/bp_usage/plot_karyogram b/bp_usage/plot_karyogram deleted file mode 100644 index 9da3c93..0000000 --- a/bp_usage/plot_karyogram +++ /dev/null @@ -1,21 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Plot hits on a karyogram for a given genome. - -Usage: ... | plot_karyogram [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-g | --genome=] - Genome layout of karyogram - Default=hg18 -Options: [-f | --feat_color=] - Color of features - Default=black -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | plot_karyogram -x -g mm8 -o plot.svg - Create plot and save to 'plot.svg'. - diff --git a/bp_usage/plot_lendist b/bp_usage/plot_lendist deleted file mode 100644 index 4cda655..0000000 --- a/bp_usage/plot_lendist +++ /dev/null @@ -1,24 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Plot length distribution. - -Usage: ... | plot_lendist [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-k | --key=] - Key to use for plotting. -Options: [-t | --terminal=] - Terminal for output: dumb|post|svg - Default=dumb -Options: [-T | --title=] - Set plot title. -Options: [-X | --xlabel=] - Set x-axis label. -Options: [-Y | --ylabel=] - Set y-axis label. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | plot_lendist -x -k HIT_LEN - Create plot and output to STDOUT in ASCII. -Examples: ... | plot_lendist -x -k HIT_LEN -t svg -o plot.svg - Create plot and save to 'plot.svg'. diff --git a/bp_usage/plot_matches b/bp_usage/plot_matches deleted file mode 100644 index 03571aa..0000000 --- a/bp_usage/plot_matches +++ /dev/null @@ -1,24 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Generate a dotplot of matches in stream. - -Usage: ... | plot_matches [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-t | --terminal= - Terminal for output: dumb|post|svg - Default=dumb -Options: [-d | --direction= - Direction of matches to plot: both|forward|reverse - Default=both -Options: [-T | --title=] - Set plot title. -Options: [-X | --xlabel=] - Set x-axis label. -Options: [-Y | --ylabel=] - Set y-axis label. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | plot_matches -x -d forward -t svg -o plot.svg - Create plot and save to 'plot.svg'. - diff --git a/bp_usage/plot_phastcons_profiles b/bp_usage/plot_phastcons_profiles deleted file mode 100644 index 3f17c95..0000000 --- a/bp_usage/plot_phastcons_profiles +++ /dev/null @@ -1,29 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: January 2008 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Generate a plot of PhastCons profiles based on chromosome coordinates in stream. - -Usage: ... | plot_phastcons_profiles [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-g | --genome=] - Genome from which to obtain PhastCons info. -Options: [-m | --mean] - Calculate a mean profile. -Options: [-M | --median] - Calculate a median profile. -Options: [-f | --flank=] - Include flanking PhastCons scores. -Options: [-t | --terminal= - Terminal for output: dumb|post|svg - Default=dumb -Options: [-d | --direction= - Direction of matches to plot: both|forward|reverse - Default=both -Options: [-T | --title=] - Set plot title. -Options: [-X | --xlabel=] - Set x-axis label. -Options: [-Y | --ylabel=] - Set y-axis label. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | plot_phastcons_profiles -x -g dm3 -f 50 - Create plot of all profiles including 50 flanking scores. -Examples: ... | plot_phastcons_profiles -x -g dm3 -f 50 -m - Create a mean plot of all profiles including 50 flanking scores. - diff --git a/bp_usage/plot_seqlogo b/bp_usage/plot_seqlogo deleted file mode 100644 index bd3ad9d..0000000 --- a/bp_usage/plot_seqlogo +++ /dev/null @@ -1,18 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Renders a sequence logo in SVG format from alignment in stream. - -Usage: ... | plot_seqlogo [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | plot_seqlogo -x -o logo.svg - Create plot and save to 'plot.svg'. diff --git a/bp_usage/random_records b/bp_usage/random_records deleted file mode 100644 index 54a7168..0000000 --- a/bp_usage/random_records +++ /dev/null @@ -1,18 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: December 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Select a number of random records from the stream. - -Usage: ... | random_records [options] - -Options: [-n | --num=] - Number of random records to select - Default=10 -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | random_records -n 100 - Output 100 random records to stream. - diff --git a/bp_usage/read_2bit b/bp_usage/read_2bit deleted file mode 100644 index 0a8c774..0000000 --- a/bp_usage/read_2bit +++ /dev/null @@ -1,26 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: March 2008 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Read sequence entries from one or more files 2bit files. The length of each sequence is also determined. - -Usage: $script [options] -i - -Options: [-i | --data_in=] - Comma separated list of files or glob expression to read. -Options: [-n | --num=] - Limit number of records to read. -Options: [-N | --no_mask] - Ignore soft masking. -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: $script -i test.2bit - Read FASTA entries from file. -Examples: $script -i test1.2bit,test2.2bit - Read FASTA entries from files. -Examples: $script -i '*.2bit' - Read FASTA entries from files. -Examples: $script -i test.2bit -n 10 - Read first 10 entries from file. - -Keys out: SEQ_NAME - Name of sequence. -Keys out: SEQ - Sequence. -Keys out: SEQ_LEN - Length of sequence. diff --git a/bp_usage/read_align b/bp_usage/read_align deleted file mode 100644 index 274a3a8..0000000 --- a/bp_usage/read_align +++ /dev/null @@ -1,29 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Read aligned FASTA entries from one or more files. The aligned sequence length is also determined. - -Usage: $script [options] -i - -Options: [-i | --data_in=] - Comma separated list of files to read. -Options: [-n | --num=] - Limit number of records to read. -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: $script -i test.fna - Read aligned FASTA entries from file. -Examples: $script -i test1.fna,test2,fna - Read aligned FASTA entries from files. -Examples: $script -i '*.fna' - Read aligned FASTA entries from files. -Examples: $script -i test.fna -n 10 - Read first 10 aligned FASTA entries from file. - -Keys out: SEQ_NAME - Name of sequence. -Keys out: SEQ - Sequence. -Keys out: ALIGN_LEN - Length of aligned sequence. -Keys out: ALIGN - Number indicating what alignment this sequence belong to. - - - diff --git a/bp_usage/read_blast_tab b/bp_usage/read_blast_tab deleted file mode 100644 index f112707..0000000 --- a/bp_usage/read_blast_tab +++ /dev/null @@ -1,33 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Read tabular BLAST output (-m 8 and -m 9). - -Usage: $script [options] -i - -Options: [-i | --data_in=] - Read input data from file. -Options: [-n | --num=] - Limit number of records to read. -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: $script --data_in=test.blast - -Keys out: Q_ID - Query ID. -Keys out: S_ID - Subject ID. -Keys out: IDENT - Identity (%). -Keys out: ALIGN_LEN - Alignment length. -Keys out: MISMATCHES - Number of mismatches. -Keys out: GAPS - Number of gaps. -Keys out: Q_BEG - Query begin. -Keys out: Q_END - Query end. -Keys out: S_BEG - Subject begin. -Keys out: S_END - Subject end. -Keys out: E_VAL - Expect value. -Keys out: BIT_SCORE - Bit score. -Keys out: STRAND - Strand. -Keys out: REC_TYPE - Record type. diff --git a/bp_usage/read_embl b/bp_usage/read_embl deleted file mode 100644 index 95a4b30..0000000 --- a/bp_usage/read_embl +++ /dev/null @@ -1,24 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: September 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Read data in EMBL format. - -Usage: $script [options] -i - -Options: [-i | --data_in=] - Read input data from file. -Options: [-n | --num=] - Limit number of records to read. -Options: [-k | --keys=] - Match a subset of record keys only. -Options: [-f | --feats=] - Match a subset of features only. -Options: [-q | --quals=] - Match a subset of qualifiers only. -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: $script -i embl.dat - Read keys, features, and qualifiers. -Examples: $script -i embl.dat -k AC,DE - Read only Accession number and Description. -Examples: $script -i embl.dat -k FT,SEQ -f CDS - Read subset of features matching CDS. -Examples: $script -i embl.dat -k FT,SEQ -f CDS -q gene - Read subset of qualifiers matching gene. diff --git a/bp_usage/read_gff b/bp_usage/read_gff deleted file mode 100644 index f9957fb..0000000 --- a/bp_usage/read_gff +++ /dev/null @@ -1,31 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: February 2008 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Read Generic Feature Format (GFF v.3) from one or more files. - -Usage: $script [options] -i - -Options: [-i | --data_in=] - Comma separated list of files or glob expression to read. -Options: [-n | --num=] - Limit number of records to read. -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: $script -i test.gff - Read GFF entries from file. - -Keys out: - -Keys out: Q_ID - Feature ID. -Keys out: SOURCE - Feature source. -Keys out: TYPE - Feature type. -Keys out: Q_BEG - Begin position -Keys out: Q_END - End position -Keys out: SCORE - Score. -Keys out: STRAND - Strand. -Keys out: PHASE - Phase. -Keys out: ATT - Attributes. -Keys out: ATT_ - Breakdown of Attributes into key/value pairs diff --git a/bp_usage/read_mysql b/bp_usage/read_mysql deleted file mode 100644 index 06f7224..0000000 --- a/bp_usage/read_mysql +++ /dev/null @@ -1,23 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: May 2008 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Read records from a MySQL query. - -Usage: $script [options] - -Options: [-d | --database=] - MySQL database. -Options: [-q | --query=] - MySQL query. -Options: [-u | --user=] - MySQL user name - Default= -Options: [-p | --password=] - MySQL password - Default= -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: $script -d dm3 -q 'SHOW TABLES' - Retreive table information from database. -Examples: $script -d dm3 -q 'SELECT * FROM estOrientInfo' - Retreive entire estOreintInfo. -Examples: $script -d dm3 -q 'SELECT * FROM table WHERE Score < 100' - Retreive selected lines from table. - diff --git a/bp_usage/read_phastcons b/bp_usage/read_phastcons deleted file mode 100644 index 268f0f4..0000000 --- a/bp_usage/read_phastcons +++ /dev/null @@ -1,38 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: December 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Read data in PhastCons format which are included in the stream as BED records. - -Usage: $script [options] -i - -Options: [-i | --data_in=] - Read input data from file. -Options: [-n | --num=] - Limit number of records to read and output. -Options: [-m | --min=] - Minimum length of a conserved block - Default=10 -Options: [-d | --dist=] - Maximum distance between conserved blocks - Default=25 -Options: [-t | --threshold=] - Threshold for conserved block - Default=0.8 -Options: [-g | --gap=] - Allow micro-gap in a conserved block - Default=5 -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: $script -i chr4.pp - -Keys out: CHR - Chromosome name. -Keys out: CHR_BEG - Chromosome begin position. -Keys out: CHR_END - Chromoeoms end position. -Keys out: Q_ID - Query ID (feature name). -Keys out: SCORE - Score. -Keys out: STRAND - Strand. -Keys out: THICK_BEG - The starting position at which the feature is drawn thickly. -Keys out: THICK_END - The ending position at which the feature is drawn thickly. -Keys out: ITEMRGB - An RGB value of the form R,G,B (e.g. 255,0,0). -Keys out: BLOCKCOUNT - The number of blocks (exons) in the BED entry. -Keys out: BLOCKSIZES - A comma separated list of the block sizes. -Keys out: Q_BEGS - A comma separated list of block starts. -Keys out: REC_TYPE - Record type. -Keys out: BED_LEN - Length of BED entry. -Keys out: BED_COLS - Number of columns in BED line. diff --git a/bp_usage/read_psl b/bp_usage/read_psl deleted file mode 100644 index cdd06a7..0000000 --- a/bp_usage/read_psl +++ /dev/null @@ -1,43 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Read PSL data (BLAT's default output). - -Usage: $script [options] -i - -Options: [-i | --data_in=] - Read PSL data from file. -Options: [-n | --num=] - Limit number of records to read. -Options: [-I | --stream_in=] - Read input stream from file - Default=STDIN -Options: [-O | --stream_out=] - Write output stream to file - Default=STDOUT - -Examples: $script -i test1.psl,test2.psl -Examples: $script -i '*.psl' - -Keys out: MATCHES - Number of non-repeat matches. -Keys out: MISMATCHES - Number of mismatches. -Keys out: REPMATCHES - Number of repeat matches. -Keys out: NCOUNT - Number of Ns. -Keys out: QNUMINSERT - Number of inserts in query. -Keys out: QBASEINSERT - Number of bases inserted in query. -Keys out: SNUMINSERT - Number of inserts in subject. -Keys out: SBASEINSERT - Number of bases inserted in subject. -Keys out: STRAND - Strand. -Keys out: Q_ID - Query ID. -Keys out: Q_LEN - Query length. -Keys out: Q_BEG - Query begin. -Keys out: Q_END - Query end. -Keys out: S_ID - Subject ID. -Keys out: S_LEN - Subject length. -Keys out: S_BEG - Subject begin. -Keys out: S_END - Subject end. -Keys out: BLOCKCOUNT - Block count. -Keys out: BLOCKSIZES - Block sizes. -Keys out: Q_BEGS - Query sequence blocks begins. -Keys out: S_BEGS - Subject sequence blocks begins. -Keys out: SCORE - Score calculated as in web BLAT results. -Keys out: REC_TYPE - Record type. -- 2.39.5