[med-svn] [iva] 01/01: applied delay patches

[Jorge Soares]

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jssoares-guest pushed a commit to branch master
in repository iva.

commit cd6e5252e3c3ab8d69805ca511dd15aa94407a67
Author: Jorge Soares <j.s.soares at gmail.com>
Date:   Fri Nov 21 10:46:24 2014 +0000

    applied delay patches
---
 debian/control                                     |  3 +-
 ...ules-in-scripts-to-generate-manpages-from-usage | 91 ++++++++++++++++++++++
 patches/series                                     |  1 +
 3 files changed, 94 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 742e253..e606a04 100644
--- a/debian/control
+++ b/debian/control
@@ -11,11 +11,12 @@ Build-Depends: debhelper (>= 9),
                python3-nose,
 	       python3-networkx,
 	       python-pysam,
-	       fastaq,
 	       samtools,
 	       mummer,
 	       smalt,
+	       fastaq,
 	       trimmomatic,
+	       bioperl,
 	       help2man
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/iva.git
diff --git a/patches/delaying-import-of-iva-modules-in-scripts-to-generate-manpages-from-usage b/patches/delaying-import-of-iva-modules-in-scripts-to-generate-manpages-from-usage
new file mode 100644
index 0000000..aea9e58
--- /dev/null
+++ b/patches/delaying-import-of-iva-modules-in-scripts-to-generate-manpages-from-usage
@@ -0,0 +1,91 @@
+Description: Delays import of several modules.
+This allows manpage creation directly form the scripts usage
+statementsIndex: iva/scripts/iva
+===================================================================
+--- iva.orig/scripts/iva
++++ iva/scripts/iva
+@@ -1,12 +1,6 @@
+ #!/usr/bin/env python3
+ 
+ import argparse
+-import os
+-import sys
+-import multiprocessing
+-import fastaq
+-import iva
+-
+ 
+ parser = argparse.ArgumentParser(
+     usage = '%(prog)s [options] {-f reads_fwd -r reads_rev | --fr reads} <output directory>')
+@@ -69,6 +63,14 @@ other_group.add_argument('--strand_bias'
+ other_group.add_argument('--version', action='version', version=iva.common.version)
+ 
+ options = parser.parse_args()
++
++
++import os
++import sys
++import multiprocessing
++import fastaq
++import iva
++
+ if options.seed_stop_length == 0:
+     options.seed_stop_length = int(0.9 * options.max_insert)
+ 
+Index: iva/scripts/iva_qc
+===================================================================
+--- iva.orig/scripts/iva_qc
++++ iva/scripts/iva_qc
+@@ -1,9 +1,6 @@
+ #!/usr/bin/env python3
+ 
+ import argparse
+-import os
+-import sys
+-import iva
+ 
+ parser = argparse.ArgumentParser(
+     usage = '%(prog)s [options] {(-f <reads_1.fq> -r <reads_2.fq>) | --fr reads.fq} {(--embl_dir | --ref_db) <directory>} <assembly.fasta> <prefix of output files>',
+@@ -17,7 +14,6 @@ ref_group = parser.add_argument_group('R
+ ref_group.add_argument('--embl_dir', help='Directory of reference EMBL files. If not used, must use --ref_db', metavar='Directory')
+ ref_group.add_argument('--ref_db', help='Directory of database made by iva_qc_make_db. If not used, must use --embl_dir', metavar='Directory')
+ 
+-
+ reads_group = parser.add_argument_group('Reads options (REQUIRED: either --fr, or (-f and -r))')
+ reads_group.add_argument('-f', '--reads_fwd', action=iva.common.abspathAction, help='Name of forwards reads fasta or fastq file. Must be used with --reads_rev', metavar='filename[.gz]')
+ reads_group.add_argument('-r', '--reads_rev', action=iva.common.abspathAction, help='Name of reverse reads fasta or fastq file. Must be used with --reads_rev', metavar='filename[.gz]')
+@@ -54,6 +50,10 @@ other_group.add_argument('--version', ac
+ options = parser.parse_args()
+ 
+ 
++import os
++import sys
++import iva
++
+ if options.embl_dir == options.ref_db == None:
+     print('You must use one of --embl_dir or --ref_db. Cannot continue.', file=sys.stderr)
+     sys.exit(1)
+Index: iva/scripts/iva_qc_make_db
+===================================================================
+--- iva.orig/scripts/iva_qc_make_db
++++ iva/scripts/iva_qc_make_db
+@@ -1,8 +1,6 @@
+ #!/usr/bin/env python3
+ 
+-import sys
+ import argparse
+-import iva
+ 
+ parser = argparse.ArgumentParser(
+     usage = '%(prog)s [options] <output directory>',
+@@ -18,6 +16,10 @@ parser.add_argument('--verbose', action=
+ parser.add_argument('--version', action='version', version=iva.common.version)
+ options = parser.parse_args()
+ 
++
++import sys
++import iva
++
+ iva.external_progs.write_prog_info('iva_qc_make_db', '-')
+ 
+ db = iva.kraken.Database(
diff --git a/patches/series b/patches/series
new file mode 100644
index 0000000..ee5e4bc
--- /dev/null
+++ b/patches/series
@@ -0,0 +1 @@
+delaying-import-of-iva-modules-in-scripts-to-generate-manpages-from-usage

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