[med-svn] [fastaq] 01/01: removed .pc directory from debian package
Jorge Soares
jssoares-guest at moszumanska.debian.org
Fri Nov 21 09:39:28 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a commit to branch master
in repository fastaq.
commit 86db77ee6baa479f5bc2e2a4052ebb6051b5d038
Author: Jorge Soares <j.s.soares at gmail.com>
Date: Fri Nov 21 09:39:07 2014 +0000
removed .pc directory from debian package
---
.pc/.quilt_patches | 1 -
.pc/.quilt_series | 1 -
.pc/.version | 1 -
.pc/applied-patches | 1 -
.../.timestamp | 0
.../scripts/fastaq_capillary_to_pairs | 12 ---
.../scripts/fastaq_chunker | 21 -----
.../scripts/fastaq_count_sequences | 11 ---
.../scripts/fastaq_deinterleave | 14 ----
.../scripts/fastaq_enumerate_names | 19 -----
.../scripts/fastaq_expand_nucleotides | 15 ----
.../scripts/fastaq_extend_gaps | 13 ---
.../scripts/fastaq_fasta_to_fastq | 13 ---
.../scripts/fastaq_filter | 24 ------
.../scripts/fastaq_get_ids | 12 ---
.../scripts/fastaq_get_seq_flanking_gaps | 14 ----
.../scripts/fastaq_insert_or_delete_bases | 94 ----------------------
.../scripts/fastaq_interleave | 13 ---
.../scripts/fastaq_long_read_simulate | 50 ------------
.../scripts/fastaq_make_random_contigs | 25 ------
.../scripts/fastaq_merge | 18 -----
.../scripts/fastaq_replace_bases | 14 ----
.../scripts/fastaq_reverse_complement | 12 ---
.../scripts/fastaq_scaffolds_to_contigs | 13 ---
.../scripts/fastaq_search_for_seq | 13 ---
.../scripts/fastaq_sequence_trim | 25 ------
.../scripts/fastaq_split_by_base_count | 15 ----
.../scripts/fastaq_strip_illumina_suffix | 12 ---
.../scripts/fastaq_to_fake_qual | 18 -----
.../scripts/fastaq_to_fasta | 19 -----
.../scripts/fastaq_to_mira_xml | 12 ---
.../scripts/fastaq_to_orfs_gff | 13 ---
.../scripts/fastaq_to_perfect_reads | 86 --------------------
.../scripts/fastaq_to_random_subset | 36 ---------
.../scripts/fastaq_to_tiling_bam | 79 ------------------
.../scripts/fastaq_to_unique_by_id | 12 ---
.../scripts/fastaq_translate | 13 ---
.../scripts/fastaq_trim_Ns_at_end | 12 ---
.../scripts/fastaq_trim_ends | 14 ----
39 files changed, 790 deletions(-)
diff --git a/.pc/.quilt_patches b/.pc/.quilt_patches
deleted file mode 100644
index 6857a8d..0000000
--- a/.pc/.quilt_patches
+++ /dev/null
@@ -1 +0,0 @@
-debian/patches
diff --git a/.pc/.quilt_series b/.pc/.quilt_series
deleted file mode 100644
index c206706..0000000
--- a/.pc/.quilt_series
+++ /dev/null
@@ -1 +0,0 @@
-series
diff --git a/.pc/.version b/.pc/.version
deleted file mode 100644
index 0cfbf08..0000000
--- a/.pc/.version
+++ /dev/null
@@ -1 +0,0 @@
-2
diff --git a/.pc/applied-patches b/.pc/applied-patches
deleted file mode 100644
index dfa3826..0000000
--- a/.pc/applied-patches
+++ /dev/null
@@ -1 +0,0 @@
-delay-import-statements-for-manpage-creation.patch
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/.timestamp b/.pc/delay-import-statements-for-manpage-creation.patch/.timestamp
deleted file mode 100644
index e69de29..0000000
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_capillary_to_pairs b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_capillary_to_pairs
deleted file mode 100755
index 0d4a48f..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_capillary_to_pairs
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Given a fasta/q file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with /1 and /2',
- usage = '%(prog)s <infile> <outfiles prefix>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outprefix', help='Prefix of output files', metavar='outfiles prefix')
-options = parser.parse_args()
-tasks.capillary_to_pairs(options.infile, options.outprefix)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_chunker b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_chunker
deleted file mode 100755
index d1aeb68..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_chunker
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Splits a multi fasta/q file into separate files. Splits sequences into chunks of a fixed size. Aims for chunk_size chunks in each file, but allows a little extra, so chunk can be up to (chunk_size + tolerance), to prevent tiny chunks made from the ends of sequences',
- usage = '%(prog)s [options] <fasta/q in> <prefix of output files> <chunk size> <tolerance>')
-parser.add_argument('infile', help='Name of input fasta/q file to be split')
-parser.add_argument('outprefix', help='Name of output fasta/q file')
-parser.add_argument('chunk_size', type=int, help='Size of each chunk')
-parser.add_argument('tolerance', type=int, help='Tolerance allowed in chunk size')
-parser.add_argument('--skip_all_Ns', action='store_true', help='Do not output any sequence that consists of all Ns')
-options = parser.parse_args()
-tasks.split_by_fixed_size(
- options.infile,
- options.outprefix,
- options.chunk_size,
- options.tolerance,
- skip_if_all_Ns=options.skip_all_Ns
-)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_count_sequences b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_count_sequences
deleted file mode 100755
index fcb7911..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_count_sequences
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Counts the number of sequences in a fasta/q file',
- usage = '%(prog)s <fasta/q in>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-options = parser.parse_args()
-print(tasks.count_sequences(options.infile))
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_deinterleave b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_deinterleave
deleted file mode 100755
index a28c505..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_deinterleave
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Deinterleaves fasta/q file, so that reads are written alternately between two output files',
- usage = '%(prog)s [options] <fasta/q in> <out_fwd> <out_rev>')
-parser.add_argument('--fasta_out', action='store_true', help='Use this to write output as fasta (default is same as input)', default=False)
-parser.add_argument('infile', help='Name of fasta/q file to be deinterleaved')
-parser.add_argument('out_fwd', help='Name of output fasta/q file of forwards reads')
-parser.add_argument('out_rev', help='Name of output fasta/q file of reverse reads')
-options = parser.parse_args()
-tasks.deinterleave(options.infile, options.out_fwd, options.out_rev, fasta_out=options.fasta_out)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_enumerate_names b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_enumerate_names
deleted file mode 100755
index 89831cb..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_enumerate_names
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Renames sequences in a file, calling them 1,2,3... etc',
- usage = '%(prog)s [options] <fasta/q in> <fasta/q out>')
-parser.add_argument('--start_index', type=int, help='Starting number [%(default)s]', default=1)
-parser.add_argument('--rename_file', help='If used, will write a file of old name to new name')
-parser.add_argument('--keep_suffix', action='store_true', help='Use this to keep a /1 or /2 suffix at the end of each name')
-parser.add_argument('infile', help='Name of fasta/q file to be read')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.enumerate_names(options.infile,
- options.outfile,
- start_index=options.start_index,
- keep_illumina_suffix=options.keep_suffix,
- rename_file=options.rename_file)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_expand_nucleotides b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_expand_nucleotides
deleted file mode 100755
index 2dbde36..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_expand_nucleotides
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Makes all combinations of sequences in input file by using all possibilities of redundant bases. e.g. ART could be AAT or AGT. Assumes input is nucleotides, not amino acids',
- usage = '%(prog)s <infile> <outfile>')
-parser.add_argument('infile', help='Name of input file. Can be any of FASTA, FASTQ, GFF3, EMBL, GBK, Phylip')
-parser.add_argument('outfile', help='Name of output file')
-options = parser.parse_args()
-tasks.expand_nucleotides(
- options.infile,
- options.outfile,
-)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_extend_gaps b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_extend_gaps
deleted file mode 100755
index e8622c3..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_extend_gaps
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Extends the length of all gaps (and trims the start/end of sequences) in a fasta/q file. Does this by replacing a set number of bases either side of each gap with Ns. Any sequence that ends up as all Ns is lost',
- usage = '%(prog)s [options] <fasta/q in> <fasta/q out>')
-parser.add_argument('--trim_number', type=int, help='Number of bases to trim around each gap, and off ends of each sequence [%(default)s]', default=100)
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.extend_gaps(options.infile, options.outfile, options.trim_number)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_fasta_to_fastq b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_fasta_to_fastq
deleted file mode 100755
index 18b6edb..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_fasta_to_fastq
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Given a fasta and qual file, makes a fastq file',
- usage = '%(prog)s <fasta in> <qual in> <fastq out>')
-parser.add_argument('fasta', help='Name of input fasta file', metavar='fasta in')
-parser.add_argument('qual', help='Name of input quality scores file', metavar='qual in')
-parser.add_argument('outfile', help='Name of output fastq file', metavar='fastq out')
-options = parser.parse_args()
-tasks.fasta_to_fastq(options.fasta, options.qual, options.outfile)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_filter b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_filter
deleted file mode 100755
index cb260e6..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_filter
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Filters a fasta/q file by sequence length and/or by name matching a regular expression',
- usage = '%(prog)s [options] <infile> <outfile>')
-parser.add_argument('--min_length', type=int, help='Minimum length of sequence to keep [%(default)s]', default=0, metavar='INT')
-parser.add_argument('--max_length', type=float, help='Maximum length of sequence to keep [%(default)s]', default=float('inf'), metavar='INT')
-parser.add_argument('--regex', help='If given, only reads with a name matching the regular expression will be kept')
-parser.add_argument('--ids_file', help='If given, only reads whose ID is in th given file will be used. One ID per line of file.')
-parser.add_argument('-v', '--invert', action='store_true', help='Keep sequences that do not match the filters')
-parser.add_argument('infile', help='Name of fasta/q file to be filtered')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.filter(options.infile,
- options.outfile,
- minlength=options.min_length,
- maxlength=options.max_length,
- regex=options.regex,
- ids_file=options.ids_file,
- invert=options.invert
-)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_get_ids b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_get_ids
deleted file mode 100755
index 59b9e0e..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_get_ids
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Gets IDs from each sequence in a fasta or fastq file',
- usage = '%(prog)s <infile> <outfile>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output file')
-options = parser.parse_args()
-tasks.get_ids(options.infile, options.outfile)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_get_seq_flanking_gaps b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_get_seq_flanking_gaps
deleted file mode 100755
index 0c54154..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_get_seq_flanking_gaps
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Gets the sequences either side of gaps in a fasta/q file',
- usage = '%(prog)s [options] <fasta/q in> <fasta/q out>')
-parser.add_argument('--left', type=int, help='Number of bases to get to left of gap [%(default)s]', default=25, metavar='INT')
-parser.add_argument('--right', type=int, help='Number of bases to get to right of gap [%(default)s]', default=25, metavar='INT')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.get_seqs_flanking_gaps(options.infile, options.outfile, options.left, options.right)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_insert_or_delete_bases b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_insert_or_delete_bases
deleted file mode 100755
index 61e1e80..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_insert_or_delete_bases
+++ /dev/null
@@ -1,94 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import sys
-import random
-from fastaq import sequences, utils, intervals
-
-parser = argparse.ArgumentParser(
- description = 'Deletes or inserts bases at given position(s) from a fasta/q file',
- usage = '%(prog)s <fasta/q in> <outfile>')
-parser.add_argument('infile', help='Name of fasta/q file to be read')
-parser.add_argument('outfile', help='Name of output file')
-parser.add_argument('-d','--delete', action='append', help='Delete the given bases from the given sequence. Format same as samtools view: name:start-end. This option can be used multiple times (once for each region to delete). Overlapping coords will be merged before deleting', metavar='Name:start:bases')
-parser.add_argument('--delete_range', help='Deletes bases starting at position P in each sequence of the input file. Deletes start + (n-1)*step bases from sequence n.', metavar='P,start,step')
-parser.add_argument('-i','--insert', action='append', help='Insert a random string of bases at the given position. Format is name:position:number_to_add. Bases are added after the position. This option can be used multiple times', metavar='Name:start:bases')
-parser.add_argument('--insert_range', help='Inserts random bases starting after position P in each sequence of the input file. Inserts start + (n-1)*step bases into sequence n.', metavar='P,start,step')
-options = parser.parse_args()
-
-test_ops = [int(x is not None) for x in [options.delete, options.insert, options.delete_range, options.insert_range]]
-
-if sum(test_ops) != 1:
- print('Must use one of --delete, --insert, --delete_range, --insert_range. Cannot continue', file=sys.stderr)
- sys.exit(1)
-
-
-def range2dic(range_in):
- if range_in is None:
- return {}
- (pos, start, step) = range_in.split(',')
- d = {}
- d['pos'] = int(pos) - 1
- d['bases'] = int(start)
- d['step'] = int(step)
- return d
-
-delete_range = range2dic(options.delete_range)
-insert_range = range2dic(options.insert_range)
-
-
-# convert the -d regions into sequence name, start and end coords
-to_delete = {}
-if options.delete:
- for s in options.delete:
- id, coords = s.rsplit(':')
- start, end = [int(x)-1 for x in coords.split('-')]
- if id not in to_delete:
- to_delete[id] = []
- to_delete[id].append(intervals.Interval(start, end))
-
-
-to_insert = {}
-if options.insert:
- for s in options.insert:
- id, pos, bases = s.rsplit(':',2)
- pos = int(pos) - 1
- bases = int(bases)
- if id not in to_insert:
- to_insert[id] = []
- to_insert[id].append((pos, bases))
-
-
-assert len(to_delete) * len(to_insert) == 0
-
-# merge overlapping regions to be deleted
-for l in to_delete.values():
- intervals.merge_overlapping_in_list(l)
-
-# sort positions to be inserted
-for l in to_insert.values():
- l.sort()
-
-# read in the fasta/q file and print outfile with deleted sequences
-seq_reader = sequences.file_reader(options.infile)
-f = utils.open_file_write(options.outfile)
-
-for seq in seq_reader:
- if seq.id in to_delete:
- # delete regions for this sequence, but start at the end so the
- # coords don't get messed up after the first deletion
- for inter in reversed(to_delete[seq.id]):
- seq.seq = seq.seq[:inter.start] + seq.seq[inter.end + 1:]
- elif options.delete_range:
- seq.seq = seq.seq[:delete_range['pos']] + seq.seq[delete_range['pos'] + delete_range['bases']:]
- delete_range['bases'] += delete_range['step']
- elif seq.id in to_insert:
- for pos, bases in reversed(to_insert[seq.id]):
- seq.seq = seq.seq[:pos + 1] + ''.join([random.choice('ACGT') for x in range(bases)]) + seq.seq[pos + 1:]
- elif options.insert_range:
- seq.seq = seq.seq[:insert_range['pos'] + 1] + ''.join([random.choice('ACGT') for x in range(insert_range['bases'])]) + seq.seq[insert_range['pos'] + 1:]
- insert_range['bases'] += insert_range['step']
-
- print(seq, file=f)
-
-utils.close(f)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_interleave b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_interleave
deleted file mode 100755
index 4b39a3e..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_interleave
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Interleaves two fasta/q files, so that reads are written alternately first/second in output file',
- usage = '%(prog)s [options] <fasta/q 1> <fasta/q 2> <outfile>')
-parser.add_argument('infile_1', help='Name of first input fasta/q file')
-parser.add_argument('infile_2', help='Name of second input fasta/q file')
-parser.add_argument('outfile', help='Name of output fasta/q file of interleaved reads')
-options = parser.parse_args()
-tasks.interleave(options.infile_1, options.infile_2, options.outfile)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_long_read_simulate b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_long_read_simulate
deleted file mode 100755
index 23106f3..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_long_read_simulate
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Simulates long reads from a fasta/q file. Can optionally make insertions into the reads, like pacbio does. If insertions made, coverage calculation is done before the insertions (so total read length may appear longer then expected).',
- usage = '%(prog)s [options] <infile> <outfile>')
-
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output fasta file')
-
-parser.add_argument('--method', help='How to sample the read positions and lengths. Choose from 1) "tiling", where reads of fixed length are taken at equal intervals from the reference. 2) "unfiform", where reads of fixed length taken at positions sampled uniformly. 3) "gamma", where reads lengths are taken from a gamma distribution, and positions sampled uniformly. [%(default)s]', default='tiling', choices=['tiling', 'uniform', 'gamma'], metavar='tiling|uniform|gamma')
-parser.add_argument('--seed', type=int, help='Seed for random number generator [default: use python\'s default]', metavar='INT')
-parser.add_argument('--qual', help='Write a file of fake quality scores called outfile.qual, all bases same quality [%(default)s]', metavar='INT')
-parser.add_argument('--fixed_read_length', type=int, help='Length of each read. Only applies if method is tile or uniform. [%(default)s]', default=20000, metavar='INT')
-parser.add_argument('--coverage', type=float, help='Read coverage. Only applies if method is gamma or uniform. [%(default)s]', default=2, metavar='FLOAT')
-
-
-tiling_group = parser.add_argument_group('tiling options')
-tiling_group.add_argument('--tile_step', type=int, help='Distance between start of each read [%(default)s]', default=10000, metavar='INT')
-
-gamma_group = parser.add_argument_group('gamma options')
-gamma_group.add_argument('--gamma_shape', type=float, help='Shape parameter of gamma distribution [%(default)s]', default=1.2, metavar='FLOAT')
-gamma_group.add_argument('--gamma_scale', type=float, help='Scale parameter of gamma distribution [%(default)s]', default=6000, metavar='FLOAT')
-gamma_group.add_argument('--gamma_min_length', type=int, help='Minimum read length [%(default)s]', default=20000, metavar='INT')
-
-ins_group = parser.add_argument_group('options to add insertions to reads')
-ins_group.add_argument('--ins_skip', type=int, help='Insert a random base every --skip bases plus or minus --ins_window. If this option is used, must also use --ins_window.', metavar='INT')
-ins_group.add_argument('--ins_window', type=int, help='See --ins_skip. If this option is used, must also use --ins_skip.', metavar='INT')
-
-
-options = parser.parse_args()
-tasks.make_long_reads(
- options.infile,
- options.outfile,
- method=options.method,
- fixed_read_length=options.fixed_read_length,
- coverage=options.coverage,
- tile_step=options.tile_step,
- gamma_shape=options.gamma_shape,
- gamma_scale=options.gamma_scale,
- gamma_min_length=options.gamma_min_length,
- seed=options.seed,
- ins_skip=options.ins_skip,
- ins_window=options.ins_window
-)
-
-if options.qual:
- tasks.fastaq_to_fake_qual(options.outfile, options.outfile + '.qual', q=options.qual)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_make_random_contigs b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_make_random_contigs
deleted file mode 100755
index c6774fe..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_make_random_contigs
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Makes a multi-fasta file of random sequences, all of the same length. Each base has equal chance of being A,C,G or T',
- usage = '%(prog)s [options] <number of sequences> <length of each sequence> <fasta out>')
-parser.add_argument('--first_number', type=int, help='If numbering the sequences, the first sequence gets this number [%(default)s]', default=1)
-parser.add_argument('--name_by_letters', action='store_true', help='Name the contigs A,B,C,... will start at A again if you get to Z')
-parser.add_argument('--prefix', help='Prefix to add to start of every sequence name', default='')
-parser.add_argument('--seed', type=int, help='Seed for random number generator. Default is to use python\'s default', default=None)
-parser.add_argument('contigs', type=int, help='Nunber of contigs to make')
-parser.add_argument('length', type=int, help='Length of each contig')
-parser.add_argument('outfile', help='Name of output file')
-options = parser.parse_args()
-tasks.make_random_contigs(
- options.contigs,
- options.length,
- options.outfile,
- name_by_letters=options.name_by_letters,
- prefix=options.prefix,
- seed=options.seed,
- first_number=options.first_number
-)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_merge b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_merge
deleted file mode 100755
index d919323..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_merge
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Converts multi fasta/q file to single sequence file, preserving original order of sequences',
- usage = '%(prog)s <infile> <outfile>')
-parser.add_argument('infile', help='Name of input file. Can be any of FASTA, FASTQ, GFF3, EMBL, GBK, Phylip')
-parser.add_argument('outfile', help='Name of output file')
-parser.add_argument('-n', '--name', help='Name of sequence in output file [%(default)s]', default='union')
-options = parser.parse_args()
-tasks.merge_to_one_seq(
- options.infile,
- options.outfile,
- seqname=options.name
-)
-
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_replace_bases b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_replace_bases
deleted file mode 100755
index 6ce2fc0..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_replace_bases
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Replaces all occurences of one letter with another in a fasta/q file',
- usage = '%(prog)s <fasta/q in> <outfile> <old> <new>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output file')
-parser.add_argument('old', help='Base to be replaced')
-parser.add_argument('new', help='Replace with this letter')
-options = parser.parse_args()
-tasks.replace_bases(options.infile, options.outfile, options.old, options.new)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_reverse_complement b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_reverse_complement
deleted file mode 100755
index 147e01f..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_reverse_complement
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Reverse complements all sequences in a fasta/q file',
- usage = '%(prog)s [options] <fasta/q in> <fasta/q out>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.reverse_complement(options.infile, options.outfile)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_scaffolds_to_contigs b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_scaffolds_to_contigs
deleted file mode 100755
index 46d4861..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_scaffolds_to_contigs
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input',
- usage = '%(prog)s [options] <infile> <outfile>')
-parser.add_argument('--number_contigs', action='store_true', help='Use this to enumerate contig names 1,2,3,... within each scaffold')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output contigs file')
-options = parser.parse_args()
-tasks.scaffolds_to_contigs(options.infile, options.outfile, number_contigs=options.number_contigs)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_search_for_seq b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_search_for_seq
deleted file mode 100755
index c00ed7a..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_search_for_seq
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Searches for an exact match on a given string and its reverese complement, in every sequences of a fasta/q file. Case insensitive. Guaranteed to find all hits',
- usage = '%(prog)s [options] <fasta/q in> <outfile> <search_string>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of outputfile. Tab-delimited output: sequence name, position, strand')
-parser.add_argument('search_string', help='String to search for in the sequences')
-options = parser.parse_args()
-tasks.search_for_seq(options.infile, options.outfile, options.search_string)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_sequence_trim b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_sequence_trim
deleted file mode 100755
index 7021c6c..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_sequence_trim
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Trims sequences off the start of all sequences in a pair of fasta/q files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming',
- usage = '%(prog)s [options] <fasta/q 1 in> <fastaq/2 in> <out 1> <out 2> <trim_seqs>')
-parser.add_argument('--min_length', type=int, help='Minimum length of output sequences [%(default)s]', default=50, metavar='INT')
-parser.add_argument('--revcomp', action='store_true', help='Trim the end of each sequence if it matches the reverse complement. This option is intended for PCR primer trimming')
-parser.add_argument('infile_1', help='Name of forward fasta/q file to be trimmed', metavar='fasta/q 1 in')
-parser.add_argument('infile_2', help='Name of reverse fasta/q file to be trimmed', metavar='fasta/q 2 in')
-parser.add_argument('outfile_1', help='Name of output forward fasta/q file', metavar='out_1')
-parser.add_argument('outfile_2', help='Name of output reverse fasta/q file', metavar='out_2')
-parser.add_argument('trim_seqs', help='Name of fasta/q file of sequences to search for at the start of each input sequence', metavar='trim_seqs')
-options = parser.parse_args()
-tasks.sequence_trim(
- options.infile_1,
- options.infile_2,
- options.outfile_1,
- options.outfile_2,
- options.trim_seqs,
- min_length=options.min_length,
- check_revcomp=options.revcomp
-)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_split_by_base_count b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_split_by_base_count
deleted file mode 100755
index dd7b43d..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_split_by_base_count
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Splits a multi fasta/q file into separate files. Does not split sequences. Puts up to max_bases into each split file. The exception is that any sequence longer than max_bases is put into its own file.',
- usage = '%(prog)s [options] <fasta/q in> <prefix of output files> <max_bases>')
-parser.add_argument('infile', help='Name of input fasta/q file to be split')
-parser.add_argument('outprefix', help='Name of output fasta/q file')
-parser.add_argument('max_bases', type=int, help='Max bases in each output split file', metavar='max_bases')
-parser.add_argument('--max_seqs', type=int, help='Max number of sequences in each output split file [no limit]', metavar='INT')
-
-options = parser.parse_args()
-tasks.split_by_base_count(options.infile, options.outprefix, options.max_bases, options.max_seqs)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_strip_illumina_suffix b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_strip_illumina_suffix
deleted file mode 100755
index 6a29a42..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_strip_illumina_suffix
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Strips /1 or /2 off the end of every read name in a fasta/q file',
- usage = '%(prog)s [options] <fasta/q in> <fasta/q out>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.strip_illumina_suffix(options.infile, options.outfile)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_fake_qual b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_fake_qual
deleted file mode 100755
index 272f7a3..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_fake_qual
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Makes fake quality scores file from a fasta/q file',
- usage = '%(prog)s <infile> <outfile>')
-parser.add_argument('infile', help='Name of input file')
-parser.add_argument('outfile', help='Name of output file')
-parser.add_argument('-q', '--qual', type=int, help='Quality score to assign to all bases [%(default)s]', default=40)
-options = parser.parse_args()
-tasks.fastaq_to_fake_qual(
- options.infile,
- options.outfile,
- q=options.qual
-)
-
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_fasta b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_fasta
deleted file mode 100755
index 742e95f..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_fasta
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Converts sequence file to FASTA format',
- usage = '%(prog)s <infile> <outfile>')
-parser.add_argument('infile', help='Name of input file. Can be any of FASTA, FASTQ, GFF3, EMBL, GBK, Phylip')
-parser.add_argument('outfile', help='Name of output file')
-parser.add_argument('-l', '--line_length', type=int, help='Number of bases on each sequence line of output file [%(default)s]', default=60)
-parser.add_argument('-s', '--strip_after_whitespace', action='store_true', help='Remove everything after first whitesapce in every sequence name')
-options = parser.parse_args()
-tasks.to_fasta(
- options.infile,
- options.outfile,
- line_length=options.line_length,
- strip_after_first_whitespace=options.strip_after_whitespace
-)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_mira_xml b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_mira_xml
deleted file mode 100755
index 582d669..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_mira_xml
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Creates an xml file from a fasta/q file of reads, for use with Mira assembler',
- usage = '%(prog)s [options] <fastq_in> <xml_out>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('xml_out', help='Name of output xml file')
-options = parser.parse_args()
-tasks.fastaq_to_mira_xml(options.infile, options.xml_out)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_orfs_gff b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_orfs_gff
deleted file mode 100755
index 0098023..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_orfs_gff
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Writes a GFF file of open reading frames from a fasta/q file',
- usage = '%(prog)s [options] <fasta/q in> <gff_out>')
-parser.add_argument('--min_length', type=int, help='Minimum length of ORF, in nucleotides [%(default)s]', default=300, metavar='INT')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('gff_out', help='Name of output gff file')
-options = parser.parse_args()
-tasks.fastaq_to_orfs_gff(options.infile, options.gff_out, min_length=options.min_length)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_perfect_reads b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_perfect_reads
deleted file mode 100755
index 6f3ca10..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_perfect_reads
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import random
-from math import floor, ceil
-from fastaq import sequences, utils
-import sys
-
-parser = argparse.ArgumentParser(
- description = 'Makes perfect paired end fastq reads from a fasta/q file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved fastq file.',
- usage = '%(prog)s <fasta/q in> <out.fastq> <mean insert size> <insert std deviation> <mean coverage> <read length>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output fastq file')
-parser.add_argument('mean_insert', type=int, help='Mean insert size of read pairs', metavar='mean insert size')
-parser.add_argument('insert_std', type=float, help='Standard devation of insert size', metavar='insert std deviation')
-parser.add_argument('coverage', type=float, help='Mean coverage of the reads', metavar='mean coverage')
-parser.add_argument('readlength', type=int, help='Length of each read', metavar='read length')
-parser.add_argument('--fragments', help='Write FASTA sequences of fragments (i.e. read pairs plus sequences in between them) to the given filename', metavar='FILENAME')
-parser.add_argument('--no_n', action='store_true', help='Don\'t allow any N or n characters in the reads')
-parser.add_argument('--seed', type=int, help='Seed for random number generator. Default is to use python\'s default', default=None, metavar='INT')
-options = parser.parse_args()
-
-random.seed(a=options.seed)
-
-seq_reader = sequences.file_reader(options.infile)
-fout = utils.open_file_write(options.outfile)
-pair_counter = 1
-
-if options.fragments:
- fout_frags = utils.open_file_write(options.fragments)
-
-for ref in seq_reader:
- # check if current seq is long enough
- if len(ref) < options.mean_insert + 4 * options.insert_std:
- print('Warning, sequence ', ref.id, ' too short. Skipping it...', file=sys.stderr)
- continue
-
- # work out how many reads to simulate
- read_pairs = int(0.5 * options.coverage * len(ref) / options.readlength)
-
- # it's possible that we pick the same fragment twice, in which case the
- # reads would get the same name. So remember the frag coords
- used_fragments = {} # (middle_position, length) => count
-
- # do the simulation: pick insert size from normal distribution, and
- # position in genome from uniform distribution
- x = 0
- while x < read_pairs:
- isize = int(random.normalvariate(options.mean_insert, options.insert_std))
- while isize > len(ref) or isize < options.readlength:
- isize = int(random.normalvariate(options.mean_insert, options.insert_std))
- middle_pos = random.randint(ceil(0.5 *isize), floor(len(ref) - 0.5 * isize))
- read_start1 = int(middle_pos - ceil(0.5 * isize))
- read_start2 = read_start1 + isize - options.readlength
-
- readname = ':'.join([ref.id, str(pair_counter), str(read_start1+1), str(read_start2+1)])
-
- fragment = (middle_pos, isize)
- if fragment in used_fragments:
- used_fragments[fragment] += 1
- readname += '.dup.' + str(used_fragments[fragment])
- else:
- used_fragments[fragment] = 1
-
- read1 = sequences.Fastq(readname + '/1', ref.seq[read_start1:read_start1 + options.readlength], 'I' * options.readlength)
- read2 = sequences.Fastq(readname + '/2', ref.seq[read_start2:read_start2 + options.readlength], 'I' * options.readlength)
-
-
- if options.no_n and ('n' in read1.seq or 'N' in read1.seq or 'n' in read2.seq or 'N' in read2.seq):
- continue
-
- read2.revcomp()
-
- print(read1, file=fout)
- print(read2, file=fout)
-
- if options.fragments:
- frag = sequences.Fasta(readname, ref.seq[read_start1:read_start2 + options.readlength])
- print(frag, file=fout_frags)
-
- pair_counter += 1
- x += 1
-
-utils.close(fout)
-if options.fragments:
- utils.close(fout_frags)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_random_subset b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_random_subset
deleted file mode 100755
index b4f11c5..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_random_subset
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env python3
-
-import sys
-import argparse
-import random
-from fastaq import sequences, utils
-
-parser = argparse.ArgumentParser(
- description = 'Takes a random subset of reads from a fasta/q file and optionally the corresponding read ' +
- 'from a mates file. Ouptut is interleaved if mates file given',
- usage = '%(prog)s [options] <fasta/q in> <outfile> <probablilty of keeping read (pair) in [0,100]>')
-parser.add_argument('--mate_file', help='Name of fasta/q mates file')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of fasta/q output file')
-parser.add_argument('probability', type=int, help='Probability of keeping any given read (pair) in [0,100]', metavar='INT')
-options = parser.parse_args()
-
-seq_reader = sequences.file_reader(options.infile)
-fout = utils.open_file_write(options.outfile)
-
-if options.mate_file:
- mate_seq_reader = sequences.file_reader(options.mate_file)
-
-for seq in seq_reader:
- if options.mate_file:
- try:
- mate_seq = next(mate_seq_reader)
- except StopIteration:
- print('Error! Didn\'t get mate for read', seq.id, file=sys.stderr)
- sys.exit(1)
- if random.randint(0, 100) <= options.probability:
- print(seq, file=fout)
- if options.mate_file:
- print(mate_seq, file=fout)
-
-utils.close(fout)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_tiling_bam b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_tiling_bam
deleted file mode 100755
index 9b9738d..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_tiling_bam
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import sys
-import os
-from fastaq import sequences, utils
-
-parser = argparse.ArgumentParser(
- description = 'Takes a fasta/q file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome',
- usage = '%(prog)s [options] <fasta/q in> <read length> <read step> <read prefix> <out.bam>',
- epilog = 'Important: assumes that samtools is in your path')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('read_length', type=int, help='Length of reads')
-parser.add_argument('read_step', type=int, help='Distance between start of each read')
-parser.add_argument('read_prefix', help='Prefix of read names')
-parser.add_argument('outfile', help='Name of output BAM file')
-parser.add_argument('--read_group', help='Add the given read group ID to all reads [%(default)s]' ,default='42')
-options = parser.parse_args()
-
-# make a header first - we need to add the @RG line to the default header made by samtools
-tmp_empty_file = options.outfile + '.tmp.empty'
-f = utils.open_file_write(tmp_empty_file)
-utils.close(f)
-try:
- f = os.popen('samtools view -H -T ' + options.infile + ' ' + tmp_empty_file)
-except IOError:
- print('Error making tmp header file', file=sys.stderr)
- sys.exit(1)
-
-header_lines = f.readlines()
-header_lines.append('@RG\tID:' + options.read_group + '\tSM:FAKE')
-f.close()
-os.unlink(tmp_empty_file)
-
-seq_reader = sequences.file_reader(options.infile)
-try:
- f = os.popen('samtools view -hbS - > ' + options.outfile, 'w')
-except IOError:
- print("Error opening for writing BAM file '" + options.outfile + "'", file=sys.stderr)
- sys.exit(1)
-
-print(''.join(header_lines), file=f)
-
-for seq in seq_reader:
- end_range = len(seq)
- if len(seq) < options.read_length:
- end_range = 1
- for i in range(0, end_range, options.read_step):
- if len(seq) <= options.read_length:
- start = 0
- end = len(seq) - 1
- else:
- start = i
- end = start + options.read_length - 1
-
- if end > len(seq) - 1:
- end = len(seq) - 1
- start = end - options.read_length + 1
-
- read = sequences.Fastq(options.read_prefix + ':' + seq.id + ':' + str(start + 1) + ':' + str(end + 1), seq[start:end+1], 'I' * (end - start + 1))
-
- print ('\t'.join([read.id,
- '0',
- seq.id,
- str(start + 1),
- '60',
- str(len(read)) + 'M',
- '*',
- '*',
- '*',
- read.seq,
- read.qual,
- 'RG:Z:' + options.read_group]), file=f)
-
- if end == len(seq) - 1:
- break
-
-f.close()
-
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_unique_by_id b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_unique_by_id
deleted file mode 100755
index e743a92..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_to_unique_by_id
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Removes duplicate sequences from a fasta/q file, based on their names. If the same name is found more than once, then the longest sequence is kept. Order of sequences is preserved in output',
- usage = '%(prog)s <infile> <outfile>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.to_unique_by_id(options.infile, options.outfile)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_translate b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_translate
deleted file mode 100755
index 9ec04c7..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_translate
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Translates all sequences in a fasta or fastq file. Output is always fasta format',
- usage = '%(prog)s <in.fasta/q> <out.fasta>')
-parser.add_argument('--frame', type=int, choices=[0,1,2], help='Frame to translate [%(default)s]', default=0)
-parser.add_argument('infile', help='Name of fasta/q file to be translated', metavar='in.fasta/q')
-parser.add_argument('outfile', help='Name of output fasta file', metavar='out.fasta')
-options = parser.parse_args()
-tasks.translate(options.infile, options.outfile, frame=options.frame)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_trim_Ns_at_end b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_trim_Ns_at_end
deleted file mode 100755
index 200d71f..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_trim_Ns_at_end
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Trims any Ns off each sequence in a fasta/q file. Does nothing to gaps in the middle, just trims the ends',
- usage = '%(prog)s [options] <fasta/q in> <fasta/q out>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.trim_Ns_at_end(options.infile, options.outfile)
diff --git a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_trim_ends b/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_trim_ends
deleted file mode 100755
index ffc662d..0000000
--- a/.pc/delay-import-statements-for-manpage-creation.patch/scripts/fastaq_trim_ends
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from fastaq import tasks
-
-parser = argparse.ArgumentParser(
- description = 'Trims set number of bases off each sequence in a fasta/q file',
- usage = '%(prog)s [options] <fasta/q in> <bases off start> <bases off end> <fasta/q out>')
-parser.add_argument('infile', help='Name of input fasta/q file')
-parser.add_argument('start_trim', type=int, help='Number of bases to trim off start')
-parser.add_argument('end_trim', type=int, help='Number of bases to trim off end')
-parser.add_argument('outfile', help='Name of output fasta/q file')
-options = parser.parse_args()
-tasks.trim(options.infile, options.outfile, options.start_trim, options.end_trim)
--
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