[med-svn] [Git][med-team/changeo][master] 8 commits: New upstream version 1.0.1
Nilesh Patra
gitlab at salsa.debian.org
Thu Oct 15 15:09:46 BST 2020
Nilesh Patra pushed to branch master at Debian Med / changeo
Commits:
fc08a33f by Nilesh Patra at 2020-10-15T13:05:08+00:00
New upstream version 1.0.1
- - - - -
d2484464 by Nilesh Patra at 2020-10-15T13:05:08+00:00
routine-update: New upstream version
- - - - -
169fa2e0 by Nilesh Patra at 2020-10-15T13:05:11+00:00
Update upstream source from tag 'upstream/1.0.1'
Update to upstream version '1.0.1'
with Debian dir 58285ea3c61c556cad5659d4c1a7027e29f249a4
- - - - -
32f183f7 by Nilesh Patra at 2020-10-15T13:05:12+00:00
routine-update: debhelper-compat 13
- - - - -
d12b640e by Nilesh Patra at 2020-10-15T13:05:51+00:00
Set upstream metadata fields: Repository.
Changes-By: lintian-brush
- - - - -
9b5bf081 by Nilesh Patra at 2020-10-15T14:07:04+00:00
Harden dependency on python3-presto
- - - - -
43f73fe8 by Nilesh Patra at 2020-10-15T14:07:42+00:00
Add manpages
- - - - -
902f953a by Nilesh Patra at 2020-10-15T14:07:48+00:00
Update changelog
- - - - -
27 changed files:
- INSTALL.rst
- NEWS.rst
- PKG-INFO
- bin/ConvertDb.py
- bin/DefineClones.py
- bin/ParseDb.py
- changeo.egg-info/PKG-INFO
- changeo.egg-info/SOURCES.txt
- changeo.egg-info/requires.txt
- changeo/IO.py
- changeo/Version.py
- − changeo/data/receptor.tsv
- + debian/AlignRecords.py.1
- + debian/AssignGenes.py.1
- + debian/BuildTrees.py.1
- + debian/ConvertDb.py.1
- + debian/CreateGermlines.py.1
- + debian/DefineClones.py.1
- + debian/MakeDb.py.1
- + debian/ParseDb.py.1
- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/manpages
- debian/rules
- debian/upstream/metadata
- requirements.txt
Changes:
=====================================
INSTALL.rst
=====================================
@@ -5,9 +5,9 @@ The simplest way to install the latest stable release of Change-O is via pip::
> pip3 install changeo --user
-The current development build can be installed using pip and mercurial in similar fashion::
+The current development build can be installed using pip and git in similar fashion::
- > pip3 install hg+https://bitbucket.org/kleinstein/changeo@default --user
+ > pip3 install git+https://bitbucket.org/kleinstein/changeo@master --user
If you currently have a development version installed, then you will likely
need to add the arguments ``--upgrade --no-deps --force-reinstall`` to the
@@ -16,14 +16,20 @@ pip3 command.
Requirements
--------------------------------------------------------------------------------
+The minimum dependencies for installation are:
+
+ `Python 3.4.0 <http://python.org>`__
+ `setuptools 2.0 <http://bitbucket.org/pypa/setuptools>`__
+ `NumPy 1.8 <http://numpy.org>`__
+ `SciPy 0.14 <http://scipy.org>`__
-+ `pandas 0.15 <http://pandas.pydata.org>`__
-+ `Biopython 1.65 <http://biopython.org>`__
-+ `presto 0.5.10 <http://presto.readthedocs.io>`__
-+ `airr 1.2.1 <https://docs.airr-community.org>`__.
++ `pandas 0.24 <http://pandas.pydata.org>`__
++ `Biopython 1.71 <http://biopython.org>`__
++ `presto 0.6.2 <http://presto.readthedocs.io>`__
++ `airr 1.2.1 <https://docs.airr-community.org>`__
+
+Some tools wrap external applications that are not required for installation.
+Those tools require minimum versions of:
+
+ AlignRecords requires `MUSCLE 3.8 <http://www.drive5.com/muscle>`__
+ ConvertDb-genbank requires `tbl2asn <https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2>`__
+ AssignGenes requires `IgBLAST 1.6 <https://ncbi.github.io/igblast>`__, but
@@ -39,7 +45,7 @@ Linux
Biopython according to its
`instructions <http://biopython.org/DIST/docs/install/Installation.html>`__.
-2. Install `presto 0.5.0 <http://presto.readthedocs.io>`__ or greater.
+2. Install `presto 0.5.10 <http://presto.readthedocs.io>`__ or greater.
3. Download the Change-O bundle and run::
@@ -75,12 +81,12 @@ Mac OS X
> brew install --env=std gfortran
-7. Install NumPy, SciPy, pandas and Biopyton using the Python package
+7. Install NumPy, SciPy, pandas and Biopython using the Python package
manager::
> pip3 install numpy scipy pandas biopython
-8. Install `presto 0.5.0 <http://presto.readthedocs.io>`__ or greater.
+8. Install `presto 0.5.10 <http://presto.readthedocs.io>`__ or greater.
9. Download the Change-O bundle, open a terminal window, change directories
to the download folder, and run::
@@ -98,7 +104,7 @@ Windows
`Unofficial Windows binary <http://www.lfd.uci.edu/~gohlke/pythonlibs>`__
collection.
-3. Install `presto 0.5.0 <http://presto.readthedocs.io>`__ or greater.
+3. Install `presto 0.5.10 <http://presto.readthedocs.io>`__ or greater.
4. Download the Change-O bundle, open a Command Prompt, change directories to
the download folder, and run::
@@ -108,16 +114,16 @@ Windows
5. For a default installation of Python 3.4, the Change-0 scripts will be
installed into ``C:\Python34\Scripts`` and should be directly
executable from the Command Prompt. If this is not the case, then
- follow step 5 below.
+ follow step 6 below.
6. Add both the ``C:\Python34`` and ``C:\Python34\Scripts`` directories
to your ``%Path%``. On Windows 7 the ``%Path%`` setting is located
under Control Panel -> System and Security -> System -> Advanced
System Settings -> Environment variables -> System variables -> Path.
-6. If you have trouble with the ``.py`` file associations, try adding ``.PY``
- to your ``PATHEXT`` environment variable. Also, opening a
- command prompt as Administrator and run::
+7. If you have trouble with the ``.py`` file associations, try adding ``.PY``
+ to your ``PATHEXT`` environment variable. Also, try opening a
+ Command Prompt as Administrator and run::
> assoc .py=Python.File
> ftype Python.File="C:\Python34\python.exe" "%1" %*
=====================================
NEWS.rst
=====================================
@@ -1,6 +1,14 @@
Release Notes
===============================================================================
+Version 1.0.1: October 13, 2020
+-------------------------------------------------------------------------------
+
++ Updated to support Biopython v1.78.
++ Increased the biopython dependency to v1.71.
++ Increased the presto dependency to 0.6.2.
+
+
Version 1.0.0: May 6, 2020
-------------------------------------------------------------------------------
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: changeo
-Version: 1.0.0
+Version: 1.0.1
Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
Home-page: http://changeo.readthedocs.io
Author: Namita Gupta, Jason Anthony Vander Heiden
=====================================
bin/ConvertDb.py
=====================================
@@ -20,7 +20,6 @@ from time import time
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
-from Bio.Alphabet import IUPAC
# Presto and changeo imports
from presto.Annotation import flattenAnnotation
@@ -70,7 +69,7 @@ def buildSeqRecord(db_record, id_field, seq_field, meta_fields=None):
desc_str = flattenAnnotation(desc_dict)
# Create SeqRecord
- seq_record = SeqRecord(Seq(db_record[seq_field], IUPAC.ambiguous_dna),
+ seq_record = SeqRecord(Seq(db_record[seq_field]),
id=desc_str, name=desc_str, description='')
return seq_record
@@ -787,8 +786,7 @@ def makeGenbankSequence(record, name=None, label=None, count_field=None, index_f
name = '%s [note=%s]' % (name, note)
# Return SeqRecord and positions
- record = SeqRecord(Seq(seq[seq_start:seq_end], IUPAC.ambiguous_dna), id=name,
- name=name, description='')
+ record = SeqRecord(Seq(seq[seq_start:seq_end]), id=name, name=name, description='')
result = {'record': record, 'start': seq_start, 'end': seq_end}
return result
=====================================
bin/DefineClones.py
=====================================
@@ -49,7 +49,7 @@ choices_distance_model = ('ham', 'aa', 'hh_s1f', 'hh_s5f',
def filterMissing(data, seq_field=junction_attr, v_field=v_attr,
j_field=j_attr, max_missing=default_max_missing):
"""
- Splits a set of sequence into passed and failed groups based on the number
+ Splits a set of sequences into passed and failed groups based on the number
of missing characters in the sequence
Arguments:
@@ -60,7 +60,7 @@ def filterMissing(data, seq_field=junction_attr, v_field=v_attr,
max_missing (int): maximum number of missing characters (non-ACGT) to permit before failing the record.
Returns:
- changeo.Multiprocessing.DbResult : objected containing filtered records.
+ changeo.Multiprocessing.DbResult : object containing filtered records.
"""
# Function to validate the sequence string
def _pass(seq):
@@ -266,17 +266,17 @@ def distanceClones(result, seq_field=default_junction_field, model=default_dista
"""
Separates a set of Receptor objects into clones
- Arguments:
+ Arguments:
result : a changeo.Multiprocessing.DbResult object with filtered records to clone
seq_field : sequence field used to calculate distance between records
model : substitution model used to calculate distance
- distance : the distance threshold to assign clonal groups
+ distance : t distance threshold to assign clonal groups
dist_mat : pandas DataFrame of pairwise nucleotide or amino acid distances
norm : normalization method
sym : symmetry method
linkage : type of linkage
- Returns:
+ Returns:
changeo.Multiprocessing.DbResult : an updated DbResult object
"""
# Get distance matrix if not provided
@@ -349,7 +349,7 @@ def collectQueue(alive, result_queue, collect_queue, db_file, fields,
"""
Assembles results from a queue of individual sequence results and manages log/file I/O
- Arguments:
+ Arguments:
alive = a multiprocessing.Value boolean controlling whether processing continues
if False exit process
result_queue : a multiprocessing.Queue holding processQueue results
@@ -556,7 +556,7 @@ def defineClones(db_file, seq_field=default_junction_field, v_field=default_v_fi
group_args['j_field'] = j_field
feed_args = {'db_file': db_file,
'reader': reader,
- 'group_func': group_func,
+ 'group_func': group_func,
'group_args': group_args}
# Define worker function and arguments
=====================================
bin/ParseDb.py
=====================================
@@ -168,7 +168,7 @@ def addDbFile(db_file, fields, values, out_file=None, out_args=default_out_args)
log['VALUES'] = ','.join(values)
printLog(log)
- # Open inut
+ # Open input
db_handle = open(db_file, 'rt')
db_iter = TSVReader(db_handle)
__, __, out_args['out_type'] = splitName(db_file)
=====================================
changeo.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: changeo
-Version: 1.0.0
+Version: 1.0.1
Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
Home-page: http://changeo.readthedocs.io
Author: Namita Gupta, Jason Anthony Vander Heiden
=====================================
changeo.egg-info/SOURCES.txt
=====================================
@@ -2,10 +2,8 @@ INSTALL.rst
LICENSE
MANIFEST.in
NEWS.rst
-PKG-INFO
README.rst
requirements.txt
-setup.cfg
setup.py
bin/AlignRecords.py
bin/AssignGenes.py
@@ -37,16 +35,4 @@ changeo/data/hh_s5f_dist.tsv
changeo/data/hs1f_compat_dist.tsv
changeo/data/m1n_compat_dist.tsv
changeo/data/mk_rs1nf_dist.tsv
-changeo/data/mk_rs5nf_dist.tsv
-changeo/data/receptor.tsv
-debian/README.Debian
-debian/changelog
-debian/changeo.lintian-overrides
-debian/control
-debian/copyright
-debian/rules
-debian/salsa-ci.yml
-debian/watch
-debian/source/format
-debian/source/options
-debian/upstream/metadata
\ No newline at end of file
+changeo/data/mk_rs5nf_dist.tsv
\ No newline at end of file
=====================================
changeo.egg-info/requires.txt
=====================================
@@ -1,8 +1,8 @@
-PyYAML>=3.12
-airr>=1.2.1
-biopython>=1.65
numpy>=1.8
-pandas>=0.24
-presto>=0.5.10
scipy>=0.14
+pandas>=0.24
+biopython>=1.71
+PyYAML>=3.12
setuptools>=2.0
+presto>=0.6.2
+airr>=1.2.1
=====================================
changeo/IO.py
=====================================
@@ -14,7 +14,6 @@ import zipfile
from itertools import chain, groupby, zip_longest
from tempfile import TemporaryDirectory
from Bio import SeqIO
-from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
# Presto and changeo imports
@@ -1058,7 +1057,7 @@ class IgBLASTReader:
# Reverse complement input sequence if required
if summary['strand'] == '-':
- seq_rc = Seq(db['sequence_input'], IUPAC.ambiguous_dna).reverse_complement()
+ seq_rc = Seq(db['sequence_input']).reverse_complement()
result['sequence_input'] = str(seq_rc)
result['rev_comp'] = 'T'
else:
=====================================
changeo/Version.py
=====================================
@@ -5,5 +5,5 @@ Version and authorship information
__author__ = 'Namita Gupta, Jason Anthony Vander Heiden'
__copyright__ = 'Copyright 2020 Kleinstein Lab, Yale University. All rights reserved.'
__license__ = 'GNU Affero General Public License 3 (AGPL-3)'
-__version__ = '1.0.0'
-__date__ = '2020.05.06'
+__version__ = '1.0.1'
+__date__ = '2020.10.13'
=====================================
changeo/data/receptor.tsv deleted
=====================================
@@ -1,111 +0,0 @@
-Name Type Description Change-O AIRR IMGT
-sequence_id Unique sequence identifier identity SEQUENCE_ID sequence_id Sequence ID
-sequence_input Query nucleotide sequence. nucleotide SEQUENCE_INPUT sequence Sequence
-sequence_vdj Aligned V(D)J sequence. nucleotide SEQUENCE_VDJ ['V-D-J-REGION', 'V-J-REGION', 'V-REGION']
-sequence_imgt IMGT-gapped, aligned V(D)J sequence. nucleotide SEQUENCE_IMGT sequence_alignment ['V-D-J-REGION', 'V-J-REGION', 'V-REGION']
-junction Junction region nucleotide sequence. nucleotide JUNCTION junction JUNCTION
-junction_aa Junction region amino acid sequence. aminoacid JUNCTION_AA junction_aa AA JUNCTION
-junction_start Start position of the junction in the query sequence. integer JUNCTION start
-junction_end End position of the junction in the query sequence. integer JUNCTION end
-junction_length Number of nucleotides in the junction region. integer JUNCTION_LENGTH junction_length JUNCTION-nt nb
-germline_vdj Inferred germline sequence aligned with the 'sequence_align' field. nucleotide GERMLINE_VDJ
-germline_vdj_d_mask Inferred germline sequence aligned with the 'sequence_align' field and having the D segment masked. nucleotide GERMLINE_VDJ_D_MASK
-germline_imgt Inferred germline sequence aligned with the 'sequence_imgt' field. nucleotide GERMLINE_IMGT germline_alignment
-germline_imgt_d_mask Inferred germline sequence aligned with the 'sequence_imgt' field and having the D segment masked. nucleotide GERMLINE_IMGT_D_MASK germline_alignment_d_mask
-v_call V gene with allele. identity V_CALL v_call V-GENE and allele
-d_call D gene with allele. identity D_CALL d_call D-GENE and allele
-j_call J gene with allele. identity J_CALL j_call J-GENE and allele
-c_call C region with allele. identity C_CALL c_call
-locus Gene locus. identity LOCUS locus
-rev_comp True if the the alignment is on the opposite strand (reverse complemented). boolean REV_COMP rev_comp Orientation
-functional True if the V(D)J sequence is a functional gene and is predicted to be productive. boolean FUNCTIONAL productive V-DOMAIN Functionality
-in_frame True if the V and J segment alignments are in-frame. boolean IN_FRAME vj_in_frame JUNCTION frame
-stop True if the aligned sequence contains a stop codon. boolean STOP stop_codon V-DOMAIN Functionality comment
-mutated_invariant True the aligment contains a mutated conserved amino acid. boolean MUTATED_INVARIANT mutated_invariant ['V-DOMAIN Functionality comment', 'V-REGION potential ins/del']
-indels True if the V(D)J sequence contains insertions and/or deletions. boolean INDELS indels ['V-REGION potential ins/del', 'V-REGION insertions', 'V-REGION deletions']
-v_seq_start Start position of the V segment in the query sequence. integer V_SEQ_START v_sequence_start V-REGION start
-v_seq_end End of the V segment in the query sequence. integer v_sequence_end V-REGION end
-v_seq_length Length of the V segment in the query sequence. integer V_SEQ_LENGTH
-v_germ_start_vdj Alignment start position in the V reference sequence. integer V_GERM_START_VDJ
-v_germ_end_vdj Alignment end position in the V reference sequence. integer
-v_germ_length_vdj Alignment length in the V reference sequence. integer V_GERM_LENGTH_VDJ
-v_germ_start_imgt Alignment start position in the IMGT-gapped V reference sequence. integer V_GERM_START_IMGT v_germline_start
-v_germ_end_imgt Alignment end position in the IMGT-gapped V reference sequence. integer v_germline_end
-v_germ_length_imgt Alignment length in the IMGT-gapped V reference sequence. integer V_GERM_LENGTH_IMGT
-np1_start Start position of the nucleotides between the V and D segments or V and J segments. integer
-np1_end End position of the nucleotides between the V and D segments or V and J segments. integer
-np1_length Number of nucleotides between the V and D segments or V and J segments. integer NP1_LENGTH np1_length "[""P3'V-nt nb"", 'N-REGION-nt nb', 'N1-REGION-nt nb', ""P5'D-nt nb""]"
-d_seq_start Start position of the D segment in the query sequence. integer D_SEQ_START d_sequence_start D-REGION start
-d_seq_end End position of the D segment in the query sequence. integer d_sequence_end D-REGION end
-d_seq_length Length of the D segment in the query sequence. integer D_SEQ_LENGTH D-REGION-nt nb
-d_germ_start Alignment start position in the D reference sequence. integer D_GERM_START d_germline_start 5'D-REGION trimmed-nt nb
-d_germ_end Alignment end position in the D reference sequence. integer d_germline_end
-d_germ_length Length of the alignment to the D reference sequence. integer D_GERM_LENGTH D-REGION-nt nb
-np2_start Start position of the nucleotides between the D and J segments. integer
-np2_end End position of the nucleotides between the D and J segments. integer
-np2_length Number of nucleotides between the D and J segments. integer NP2_LENGTH np2_length "[""P3'D-nt nb"", 'N2-REGION-nt nb', ""P5'J-nt nb""]"
-j_seq_start Start position of the J segment in the query sequence. integer J_SEQ_START j_sequence_start J-REGION start
-j_seq_end End position of the J segment in the query sequence. integer j_sequence_end J-REGION end
-j_seq_length Length of the J segment in the query sequence. integer J_SEQ_LENGTH
-j_germ_start Alignment start position in the J reference sequence. integer J_GERM_START j_germline_start 5'J-REGION trimmed-nt nb
-j_germ_end Alignment start position in the J reference sequence. integer j_germline_end
-j_germ_length Alignment length of the J reference sequence. integer J_GERM_LENGTH
-np1 Nucleotide sequence of the combined N/P region between the V and D segments or V and J segments. nucleotide NP1 np1 "[""P3'V"", 'N-REGION', 'N1-REGION', ""P5'D""]"
-np2 Nucleotide sequence of the combined N/P region between the D and J segments. nucleotide NP2 np2 "[""P3'D"", 'N2-REGION', ""P5'J""]"
-fwr1 Nucleotide sequence of the aligned FWR1 region. nucleotide FWR1_IMGT fwr1 FR1-IMGT
-fwr2 Nucleotide sequence of the aligned FWR2 region. nucleotide FWR2_IMGT fwr2 FR2-IMGT
-fwr3 Nucleotide sequence of the aligned FWR3 region. nucleotide FWR3_IMGT fwr3 FR3-IMGT
-fwr4 Nucleotide sequence of the aligned FWR4 region. nucleotide FWR4_IMGT fwr4 FR4-IMGT
-cdr1 Nucleotide sequence of the aligned CDR1 region. nucleotide CDR1_IMGT cdr1 CDR1-IMGT
-cdr2 Nucleotide sequence of the aligned CDR2 region. nucleotide CDR2_IMGT cdr2 CDR2-IMGT
-cdr3 Nucleotide sequence of the aligned CDR3 region. nucleotide CDR3_IMGT cdr3 CDR3-IMGT
-fwr1_start FWR1 start position in the query sequence. integer fwr1_start FR1-IMGT start
-fwr1_end FWR1 end position in the query sequence. integer fwr1_end FR1-IMGT end
-fwr2_start FWR2 start position in the query sequence. integer fwr2_start FR2-IMGT start
-fwr2_end FWR2 end position in the query sequence. integer fwr2_end FR2-IMGT end
-fwr3_start FWR3 start position in the query sequence. integer fwr3_start FR3-IMGT start
-fwr3_end FWR3 end position in the query sequence. integer fwr3_end FR3-IMGT end
-fwr4_start FWR4 start position in the query sequence. integer fwr4_start FR4-IMGT start
-fwr4_end FWR4 end position in the query sequence. integer fwr4_end FR4-IMGT end
-cdr1_start CDR1 start position in the query sequence. integer cdr1_start CDR1-IMGT start
-cdr1_end CDR1 end position in the query sequence. integer cdr1_end CDR1-IMGT end
-cdr2_start CDR2 start position in the query sequence. integer cdr2_start CDR2-IMGT start
-cdr2_end CDR2 end position in the query sequence. integer cdr2_end CDR2-IMGT end
-cdr3_start CDR3 start position in the query sequence. integer cdr3_start CDR3-IMGT start
-cdr3_end CDR3 end position in the query sequence. integer cdr3_end CDR3-IMGT end
-v_score V alignment score. float V_SCORE v_score V-REGION score
-v_identity V alignment fractional identity. float V_IDENTITY v_identity V-REGION identity %
-v_evalue V alignment E-value. float V_EVALUE v_support
-v_cigar V alignment CIGAR string. identity V_CIGAR v_cigar
-v_btop V alignment BTOP string. identity V_BTOP
-d_score D alignment score. float D_SCORE d_score D-REGION score
-d_identity D alignment fractional identity. float D_IDENTITY d_identity D-REGION identity %
-d_evalue D alignment E-value. float D_EVALUE d_support
-d_cigar D alignment CIGAR string. identity D_CIGAR d_cigar
-d_btop D alignment BTOP string. identity D_BTOP
-j_score J alignment score. float J_SCORE j_score J-REGION score
-j_identity J alignment fractional identity. float J_IDENTITY j_identity J-REGION identity %
-j_evalue J alignment E-value. float J_EVALUE j_support
-j_cigar J alignment CIGAR string. identity J_CIGAR j_cigar
-j_btop V alignment BTOP string. identity J_BTOP
-c_score C region alignment score. float C_SCORE c_score
-c_identity C region alignment fractional identity. float C_IDENTITY c_identity
-c_evalue C region alignment E-value. float C_EVALUE c_support
-c_cigar C region alignment CIGAR string. identity C_CIGAR c_cigar
-c_btop V alignment BTOP string. identity C_BTOP
-vdj_score Alignment score for aligners that consider the full sequence. float VDJ_SCORE vdj_score
-vdj_identity Alignment fractional identity for aligners that consider the full sequence. float VDJ_IDENTITY vdj_identity
-vdj_evalue Alignment E-value for aligners that consider the full sequence. float VDJ_EVALUE vdj_support
-vdj_cigar CIGAR string for the full V(D)J alignment. identity VDJ_CIGAR vdj_cigar
-vdj_btop BTOP string for the full V(D)J alignment. identity VDJ_BTOP
-n1_length Number of untemplated nucleotides 5' of the D segment. integer N1_LENGTH n1_length ['N-REGION-nt nb', 'N1-REGION-nt nb']
-n2_length Number of untemplated nucleotides 3' of the D segment. integer N2_LENGTH n2_length N2-REGION-nt nb
-p3v_length Number of palindromic nucleotides 3' of the V segment. integer P3V_LENGTH p3v_length P3'V-nt nb
-p5d_length Number of palindromic nucleotides 5' of the D segment. integer P5D_LENGTH p5d_length P5'D-nt nb
-p3d_length Number of palindromic nucleotides 3' of the D segment. integer P3D_LENGTH p3d_length P3'D-nt nb
-p5j_length Number of palindromic nucleotides 5' of the J segment. integer P5J_LENGTH p5j_length P5'J-nt nb
-d_frame Reading frame of the D segment. integer D_FRAME D-REGION reading frame
-dupcount Copy number or number of duplicate observations of the sequence. integer DUPCOUNT duplicate_count
-conscount Number of reads contributing to the (UMI) consensus for this sequence. integer CONSCOUNT consensus_count
-clone Clonal cluster assignment for the query sequence. identity CLONE clone_id
-cell Cell identifier. identity CELL cell_id
=====================================
debian/AlignRecords.py.1
=====================================
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH ALIGNRECORDS.PY "1" "October 2020" "AlignRecords.py 1.0.1" "User Commands"
+.SH NAME
+AlignRecords.py \- Repertoire clonal assignment toolkit (Python 3)
+.SH DESCRIPTION
+usage: AlignRecords.py [\-\-version] [\-h] ...
+.PP
+Multiple aligns sequence fields
+.SS "help:"
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "subcommands:"
+.IP
+alignment method
+.TP
+across
+Multiple aligns sequence columns within groups and across rows
+using MUSCLE.
+.TP
+within
+Multiple aligns sequence fields within rows using MUSCLE
+.TP
+block
+Multiple aligns sequence groups across both columns and rows
+using MUSCLE.
+.SS "output files:"
+.IP
+align\-pass
+.IP
+database with multiple aligned sequences.
+.IP
+align\-fail
+.IP
+database with records failing alignment.
+.SS "required fields:"
+.IP
+sequence_id, v_call, j_call
+<field>
+.IP
+user specified sequence fields to align.
+.SS "output fields:"
+.IP
+<field>_align
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/AssignGenes.py.1
=====================================
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH ASSIGNGENES.PY "1" "October 2020" "AssignGenes.py 1.0.1" "User Commands"
+.SH NAME
+AssignGenes.py \- Repertoire clonal assignment toolkit (Python 3)
+.SH DESCRIPTION
+usage: AssignGenes.py [\-\-version] [\-h] ...
+.PP
+Assign V(D)J gene annotations
+.SS "help:"
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "subcommands:"
+.IP
+Assignment operation
+.TP
+igblast
+Executes igblastn.
+.IP
+igblast\-aa
+.IP
+Executes igblastp.
+.SS "output files:"
+.IP
+igblast
+.IP
+Reference alignment results from IgBLAST.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/BuildTrees.py.1
=====================================
@@ -0,0 +1,173 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH BUILDTREES.PY "1" "October 2020" "BuildTrees.py 1.0.1" "User Commands"
+.SH NAME
+BuildTrees.py \- Repertoire clonal assignment toolkit (Python 3)
+.SH DESCRIPTION
+\fI\,/usr/bin/BuildTrees\/\fP.py:488: SyntaxWarning: "is" with a literal. Did you mean "=="?
+.IP
+if germline is "":
+.PP
+\fI\,/usr/bin/BuildTrees\/\fP.py:543: SyntaxWarning: "is" with a literal. Did you mean "=="?
+.IP
+if ngermline is "":
+.PP
+\fI\,/usr/bin/BuildTrees\/\fP.py:801: SyntaxWarning: "is not" with a literal. Did you mean "!="?
+.IP
+if regions["cdr3_imgt"] is not "" and regions["cdr3_imgt"] is not None:
+.PP
+\fI\,/usr/bin/BuildTrees\/\fP.py:827: SyntaxWarning: "is not" with a literal. Did you mean "!="?
+.IP
+elif regions["fwr3_imgt"] is not "" and regions["fwr3_imgt"] is not None:
+.PP
+usage: BuildTrees.py [\-\-version] [\-h] \fB\-d\fR DB_FILES [DB_FILES ...]
+.TP
+[\-\-outdir OUT_DIR] [\-\-outname OUT_NAME] [\-\-log LOG_FILE]
+[\-\-failed] [\-\-format {airr,changeo}] [\-\-collapse]
+[\-\-ncdr3] [\-\-nmask] [\-\-md META_DATA [META_DATA ...]]
+[\-\-clones TARGET_CLONES [TARGET_CLONES ...]]
+[\-\-minseq MIN_SEQ] [\-\-sample SAMPLE_DEPTH]
+[\-\-append APPEND [APPEND ...]] [\-\-igphyml]
+[\-\-nproc NPROC] [\-\-clean {none,all}]
+[\-\-optimize {n,r,l,lr,tl,tlr}]
+[\-\-omega {e,ce,e,e,ce,e,e,ce,ce,ce}] [\-t {e,ce}]
+[\-\-motifs MOTIFS] [\-\-hotness HOTNESS]
+[\-\-oformat {tab,txt}] [\-\-nohlp] [\-\-asr ASR]
+.PP
+Converts TSV files into IgPhyML input files
+.SS "help:"
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "standard arguments:"
+.TP
+\fB\-d\fR DB_FILES [DB_FILES ...]
+A list of tab delimited database files. (default:
+None)
+.TP
+\fB\-\-outdir\fR OUT_DIR
+Specify to changes the output directory to the
+location specified. The input file directory is used
+if this is not specified. (default: None)
+.TP
+\fB\-\-outname\fR OUT_NAME
+Changes the prefix of the successfully processed
+output file to the string specified. May not be
+specified with multiple input files. (default: None)
+.TP
+\fB\-\-log\fR LOG_FILE
+Specify to write verbose logging to a file. May not be
+specified with multiple input files. (default: None)
+.TP
+\fB\-\-failed\fR
+If specified create files containing records that fail
+processing. (default: False)
+.TP
+\fB\-\-format\fR {airr,changeo}
+Specify input and output format. (default: airr)
+.SS "sequence processing arguments:"
+.TP
+\fB\-\-collapse\fR
+If specified, collapse identical sequences before
+exporting to fasta. (default: False)
+.TP
+\fB\-\-ncdr3\fR
+If specified, remove CDR3 from all sequences.
+(default: False)
+.TP
+\fB\-\-nmask\fR
+If specified, do not attempt to mask split codons.
+(default: False)
+.TP
+\fB\-\-md\fR META_DATA [META_DATA ...]
+List of fields to containing metadata to include in
+output fasta file sequence headers. (default: None)
+.TP
+\fB\-\-clones\fR TARGET_CLONES [TARGET_CLONES ...]
+List of clone IDs to output, if specified. (default:
+None)
+.TP
+\fB\-\-minseq\fR MIN_SEQ
+Minimum number of data sequences. Any clones with
+fewer than the specified number of sequences will be
+excluded. (default: 1)
+.TP
+\fB\-\-sample\fR SAMPLE_DEPTH
+Depth of reads to be subsampled (before
+deduplication). (default: \fB\-1\fR)
+.TP
+\fB\-\-append\fR APPEND [APPEND ...]
+List of columns to append to sequence ID to ensure
+uniqueness. (default: None)
+.SS "IgPhyML arguments (see igphyml -h for details):"
+.TP
+\fB\-\-igphyml\fR
+Run IgPhyML on output? (default: False)
+.TP
+\fB\-\-nproc\fR NPROC
+Number of threads to parallelize IgPhyML across.
+(default: 1)
+.TP
+\fB\-\-clean\fR {none,all}
+Delete intermediate files? none: leave all
+intermediate files; all: delete all intermediate
+files. (default: none)
+.TP
+\fB\-\-optimize\fR {n,r,l,lr,tl,tlr}
+Optimize combination of topology (t) branch lengths
+(l) and parameters (r), or nothing (n), for IgPhyML.
+(default: lr)
+.TP
+\fB\-\-omega\fR {e,ce,e,e,ce,e,e,ce,ce,ce}
+Omega parameters to estimate for FWR,CDR respectively:
+e = estimate, ce = estimate + confidence interval
+(default: e,e)
+.TP
+\fB\-t\fR {e,ce}
+Kappa parameters to estimate: e = estimate, ce =
+estimate + confidence interval (default: e)
+.TP
+\fB\-\-motifs\fR MOTIFS
+Which motifs to estimate mutability. (default:
+WRC_2:0,GYW_0:1,WA_1:2,TW_0:3,SYC_2:4,GRS_0:5)
+.TP
+\fB\-\-hotness\fR HOTNESS
+Mutability parameters to estimate: e = estimate, ce =
+estimate + confidence interval (default: e,e,e,e,e,e)
+.TP
+\fB\-\-oformat\fR {tab,txt}
+IgPhyML output format. (default: tab)
+.TP
+\fB\-\-nohlp\fR
+Don't run HLP model? (default: False)
+.TP
+\fB\-\-asr\fR ASR
+Ancestral sequence reconstruction interval (0\-1).
+(default: \fB\-1\fR)
+.SS "output files:"
+.IP
+<folder>
+.IP
+folder containing fasta and partition files for each clone.
+.IP
+lineages
+.IP
+successfully processed records.
+.IP
+lineages\-fail
+.IP
+database records failed processing.
+.IP
+igphyml\-pass
+.IP
+parameter estimates and lineage trees from running IgPhyML, if specified
+.SS "required fields:"
+.IP
+sequence_id, sequence, sequence_alignment,
+germline_alignment_d_mask or germline_alignment,
+v_call, j_call, clone_id, v_sequence_start
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/ConvertDb.py.1
=====================================
@@ -0,0 +1,64 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH CONVERTDB.PY "1" "October 2020" "ConvertDb.py 1.0.1" "User Commands"
+.SH NAME
+ConvertDb.py \- Repertoire clonal assignment toolkit (Python 3)
+.SH DESCRIPTION
+usage: ConvertDb.py [\-\-version] [\-h] ...
+.PP
+Parses tab delimited database files
+.SS "help:"
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "subcommands:"
+.IP
+Database operation
+.TP
+airr
+Converts input to an AIRR TSV file.
+.TP
+changeo
+Converts input into a Change\-O TSV file.
+.TP
+fasta
+Creates a fasta file from database records.
+.TP
+baseline
+Creates a specially formatted fasta file from database records
+for input into the BASELINe website. The format groups clonally
+related sequences sequentially, with the germline sequence
+preceding each clone and denoted by headers starting with ">>".
+.TP
+genbank
+Creates files for GenBank/TLS submissions.
+.SS "output files:"
+.IP
+airr
+.IP
+AIRR formatted database files.
+.IP
+changeo
+.IP
+Change\-O formatted database files.
+.IP
+sequences
+.IP
+FASTA formatted sequences output from the subcommands fasta and clip.
+.IP
+genbank
+.IP
+feature tables and fasta files containing MiAIRR compliant input for tbl2asn.
+.SS "required fields:"
+.IP
+sequence_id, sequence, sequence_alignment, junction, v_call, d_call, j_call,
+v_germline_start, v_germline_end, v_sequence_start, v_sequence_end,
+d_sequence_start, d_sequence_end, j_sequence_start, j_sequence_end
+.SS "optional fields:"
+.IP
+germline_alignment, c_call, clone_id
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/CreateGermlines.py.1
=====================================
@@ -0,0 +1,130 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH CREATEGERMLINES.PY "1" "October 2020" "CreateGermlines.py 1.0.1" "User Commands"
+.SH NAME
+CreateGermlines.py \- Repertoire clonal assignment toolkit (Python 3)
+.SH DESCRIPTION
+usage: CreateGermlines.py [\-\-version] [\-h] \fB\-d\fR DB_FILES [DB_FILES ...]
+.TP
+[\-o OUT_FILES [OUT_FILES ...]] [\-\-outdir OUT_DIR]
+[\-\-outname OUT_NAME] [\-\-log LOG_FILE] [\-\-failed]
+[\-\-format {airr,changeo}] \fB\-r\fR REFERENCES
+[REFERENCES ...]
+[\-g {full,dmask,vonly,regions} [{full,dmask,vonly,regions} ...]]
+[\-\-cloned] [\-\-sf SEQ_FIELD] [\-\-vf V_FIELD]
+[\-\-df D_FIELD] [\-\-jf J_FIELD] [\-\-cf CLONE_FIELD]
+.PP
+Reconstructs germline sequences from alignment data
+.SS "help:"
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "standard arguments:"
+.TP
+\fB\-d\fR DB_FILES [DB_FILES ...]
+A list of tab delimited database files. (default:
+None)
+.TP
+\fB\-o\fR OUT_FILES [OUT_FILES ...]
+Explicit output file name. Note, this argument cannot
+be used with the \fB\-\-failed\fR, \fB\-\-outdir\fR, or \fB\-\-outname\fR
+arguments. If unspecified, then the output filename
+will be based on the input filename(s). (default:
+None)
+.TP
+\fB\-\-outdir\fR OUT_DIR
+Specify to changes the output directory to the
+location specified. The input file directory is used
+if this is not specified. (default: None)
+.TP
+\fB\-\-outname\fR OUT_NAME
+Changes the prefix of the successfully processed
+output file to the string specified. May not be
+specified with multiple input files. (default: None)
+.TP
+\fB\-\-log\fR LOG_FILE
+Specify to write verbose logging to a file. May not be
+specified with multiple input files. (default: None)
+.TP
+\fB\-\-failed\fR
+If specified create files containing records that fail
+processing. (default: False)
+.TP
+\fB\-\-format\fR {airr,changeo}
+Specify input and output format. (default: airr)
+.SS "germline construction arguments:"
+.TP
+\fB\-r\fR REFERENCES [REFERENCES ...]
+List of folders and/or fasta files (with .fasta, .fna
+or .fa extension) with germline sequences. When using
+the default Change\-O sequence and coordinate fields,
+these reference sequences must contain IMGT\-numbering
+spacers (gaps) in the V segment. Alternative numbering
+schemes, or no numbering, may work for alternative
+sequence and coordinate definitions that define a
+valid alignment, but a warning will be issued.
+(default: None)
+.TP
+\fB\-g\fR {full,dmask,vonly,regions} [{full,dmask,vonly,regions} ...]
+Specify type(s) of germlines to include full germline,
+germline with D segment masked, or germline for V
+segment only. (default: ['dmask'])
+.TP
+\fB\-\-cloned\fR
+Specify to create only one germline per clone. Note,
+if allele calls are ambiguous within a clonal group,
+this will place the germline call used for the entire
+clone within the germline_v_call, germline_d_call and
+germline_j_call fields. (default: False)
+.TP
+\fB\-\-sf\fR SEQ_FIELD
+Field containing the aligned sequence. Defaults to
+sequence_alignment (airr) or SEQUENCE_IMGT (changeo).
+(default: None)
+.TP
+\fB\-\-vf\fR V_FIELD
+Field containing the germline V segment call. Defaults
+to v_call (airr) or V_CALL (changeo). (default: None)
+.TP
+\fB\-\-df\fR D_FIELD
+Field containing the germline D segment call. Defaults
+to d_call (airr) or D_CALL (changeo). (default: None)
+.TP
+\fB\-\-jf\fR J_FIELD
+Field containing the germline J segment call. Defaults
+to j_call (airr) or J_CALL (changeo). (default: None)
+.TP
+\fB\-\-cf\fR CLONE_FIELD
+Field containing clone identifiers. Ignored if
+\fB\-\-cloned\fR is not also specified. Defaults to clone_id
+(airr) or CLONE (changeo). (default: None)
+.SS "output files:"
+.IP
+germ\-pass
+.IP
+database with assigned germline sequences.
+.IP
+germ\-fail
+.IP
+database with records failing germline assignment.
+.SS "required fields:"
+.IP
+sequence_id, sequence_alignment, v_call, d_call, j_call,
+v_sequence_start, v_sequence_end, v_germline_start, v_germline_end,
+d_sequence_start, d_sequence_end, d_germline_start, d_germline_end,
+j_sequence_start, j_sequence_end, j_germline_start, j_germline_end,
+np1_length, np2_length
+.SS "optional fields:"
+.IP
+n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length,
+clone_id
+.SS "output fields:"
+.IP
+germline_v_call, germline_d_call, germline_j_call,
+germline_alignment, germline_alignment_d_mask,
+germline_alignment_v_region, germline_regions,
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/DefineClones.py.1
=====================================
@@ -0,0 +1,155 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH DEFINECLONES.PY "1" "October 2020" "DefineClones.py 1.0.1" "User Commands"
+.SH NAME
+DefineClones.py \- Repertoire clonal assignment toolkit (Python 3)
+.SH DESCRIPTION
+usage: DefineClones.py [\-\-version] [\-h] \fB\-d\fR DB_FILES [DB_FILES ...]
+.TP
+[\-o OUT_FILES [OUT_FILES ...]] [\-\-outdir OUT_DIR]
+[\-\-outname OUT_NAME] [\-\-log LOG_FILE] [\-\-failed]
+[\-\-format {airr,changeo}] [\-\-nproc NPROC]
+[\-\-sf SEQ_FIELD] [\-\-vf V_FIELD] [\-\-jf J_FIELD]
+[\-\-gf GROUP_FIELDS [GROUP_FIELDS ...]]
+[\-\-mode {allele,gene}] [\-\-act {first,set}]
+[\-\-model {ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat}]
+[\-\-dist DISTANCE] [\-\-norm {len,mut,none}]
+[\-\-sym {avg,min}] [\-\-link {single,average,complete}]
+[\-\-maxmiss MAX_MISSING]
+.PP
+Assign Ig sequences into clones
+.SS "help:"
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "standard arguments:"
+.TP
+\fB\-d\fR DB_FILES [DB_FILES ...]
+A list of tab delimited database files. (default:
+None)
+.TP
+\fB\-o\fR OUT_FILES [OUT_FILES ...]
+Explicit output file name. Note, this argument cannot
+be used with the \fB\-\-failed\fR, \fB\-\-outdir\fR, or \fB\-\-outname\fR
+arguments. If unspecified, then the output filename
+will be based on the input filename(s). (default:
+None)
+.TP
+\fB\-\-outdir\fR OUT_DIR
+Specify to changes the output directory to the
+location specified. The input file directory is used
+if this is not specified. (default: None)
+.TP
+\fB\-\-outname\fR OUT_NAME
+Changes the prefix of the successfully processed
+output file to the string specified. May not be
+specified with multiple input files. (default: None)
+.TP
+\fB\-\-log\fR LOG_FILE
+Specify to write verbose logging to a file. May not be
+specified with multiple input files. (default: None)
+.TP
+\fB\-\-failed\fR
+If specified create files containing records that fail
+processing. (default: False)
+.TP
+\fB\-\-format\fR {airr,changeo}
+Specify input and output format. (default: airr)
+.TP
+\fB\-\-nproc\fR NPROC
+The number of simultaneous computational processes to
+execute (CPU cores to utilized). (default: 8)
+.SS "cloning arguments:"
+.TP
+\fB\-\-sf\fR SEQ_FIELD
+Field to be used to calculate distance between
+records. Defaults to junction (airr) or JUNCTION
+(changeo). (default: None)
+.TP
+\fB\-\-vf\fR V_FIELD
+Field containing the germline V segment call. Defaults
+to v_call (airr) or V_CALL (changeo). (default: None)
+.TP
+\fB\-\-jf\fR J_FIELD
+Field containing the germline J segment call. Defaults
+to j_call (airr) or J_CALL (changeo). (default: None)
+.TP
+\fB\-\-gf\fR GROUP_FIELDS [GROUP_FIELDS ...]
+Additional fields to use for grouping clones aside
+from V, J and junction length. (default: None)
+.TP
+\fB\-\-mode\fR {allele,gene}
+Specifies whether to use the V(D)J allele or gene for
+initial grouping. (default: gene)
+.TP
+\fB\-\-act\fR {first,set}
+Specifies how to handle multiple V(D)J assignments for
+initial grouping. The "first" action will use only the
+first gene listed. The "set" action will use all gene
+assignments and construct a larger gene grouping
+composed of any sequences sharing an assignment or
+linked to another sequence by a common assignment
+(similar to single\-linkage). (default: set)
+.TP
+\fB\-\-model\fR {ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat}
+Specifies which substitution model to use for
+calculating distance between sequences. The "ham"
+model is nucleotide Hamming distance and "aa" is amino
+acid Hamming distance. The "hh_s1f" and "hh_s5f"
+models are human specific single nucleotide and 5\-mer
+content models, respectively, from Yaari et al, 2013.
+The "mk_rs1nf" and "mk_rs5nf" models are mouse
+specific single nucleotide and 5\-mer content models,
+respectively, from Cui et al, 2016. The "m1n_compat"
+and "hs1f_compat" models are deprecated models
+provided backwards compatibility with the "m1n" and
+"hs1f" models in Change\-O v0.3.3 and SHazaM v0.1.4.
+Both 5\-mer models should be considered experimental.
+(default: ham)
+.TP
+\fB\-\-dist\fR DISTANCE
+The distance threshold for clonal grouping (default:
+0.0)
+.TP
+\fB\-\-norm\fR {len,mut,none}
+Specifies how to normalize distances. One of none (do
+not normalize), len (normalize by length), or mut
+(normalize by number of mutations between sequences).
+(default: len)
+.TP
+\fB\-\-sym\fR {avg,min}
+Specifies how to combine asymmetric distances. One of
+avg (average of A\->B and B\->A) or min (minimum of A\->B
+and B\->A). (default: avg)
+.TP
+\fB\-\-link\fR {single,average,complete}
+Type of linkage to use for hierarchical clustering.
+(default: single)
+.TP
+\fB\-\-maxmiss\fR MAX_MISSING
+The maximum number of non\-ACGT characters (gaps or Ns)
+to permit in the junction sequence before excluding
+the record from clonal assignment. Note, under single
+linkage non\-informative positions can create
+artifactual links between unrelated sequences. Use
+with caution. (default: 0)
+.SS "output files:"
+.IP
+clone\-pass
+.IP
+database with assigned clonal group numbers.
+.IP
+clone\-fail
+.IP
+database with records failing clonal grouping.
+.SS "required fields:"
+.IP
+sequence_id, v_call, j_call, junction
+.SS "output fields:"
+.IP
+clone_id
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/MakeDb.py.1
=====================================
@@ -0,0 +1,71 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH MAKEDB.PY "1" "October 2020" "MakeDb.py 1.0.1" "User Commands"
+.SH NAME
+MakeDb.py \- Repertoire clonal assignment toolkit (Python 3)
+.SH DESCRIPTION
+usage: MakeDb.py [\-\-version] [\-h] ...
+.PP
+Create tab\-delimited database file to store sequence alignment information
+.SS "help:"
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "subcommands:"
+.IP
+Aligner used
+.TP
+igblast
+Process igblastn output.
+.IP
+igblast\-aa
+.IP
+Process igblastp output.
+.TP
+imgt
+Process IMGT/HighV\-Quest output (does not work with V\-QUEST).
+.TP
+ihmm
+Process iHMMune\-Align output.
+.SS "output files:"
+.IP
+db\-pass
+.IP
+database of alignment records with functionality information,
+V and J calls, and a junction region.
+.IP
+db\-fail
+.IP
+database with records that fail due to no productivity information,
+no gene V assignment, no J assignment, or no junction region.
+.SS "universal output fields:"
+.IP
+sequence_id, sequence, sequence_alignment, germline_alignment,
+rev_comp, productive, stop_codon, vj_in_frame, locus,
+v_call, d_call, j_call, junction, junction_length, junction_aa,
+v_sequence_start, v_sequence_end, v_germline_start, v_germline_end,
+d_sequence_start, d_sequence_end, d_germline_start, d_germline_end,
+j_sequence_start, j_sequence_end, j_germline_start, j_germline_end,
+np1_length, np2_length, fwr1, fwr2, fwr3, fwr4, cdr1, cdr2, cdr3
+.SS "imgt specific output fields:"
+.IP
+n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length,
+d_frame, v_score, v_identity, d_score, d_identity, j_score, j_identity
+.SS "igblast specific output fields:"
+.IP
+v_score, v_identity, v_support, v_cigar,
+d_score, d_identity, d_support, d_cigar,
+j_score, j_identity, j_support, j_cigar
+.SS "ihmm specific output fields:"
+.IP
+vdj_score
+.SS "10X specific output fields:"
+.IP
+cell_id, c_call, consensus_count, umi_count,
+v_call_10x, d_call_10x, j_call_10x,
+junction_10x, junction_10x_aa
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/ParseDb.py.1
=====================================
@@ -0,0 +1,68 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH PARSEDB.PY "1" "October 2020" "ParseDb.py 1.0.1" "User Commands"
+.SH NAME
+ParseDb.py \- Repertoire clonal assignment toolkit (Python 3)
+.SH DESCRIPTION
+usage: ParseDb.py [\-\-version] [\-h] ...
+.PP
+Parses tab delimited database files
+.SS "help:"
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS "subcommands:"
+.IP
+Database operation
+.TP
+add
+Adds field and value pairs.
+.TP
+delete
+Deletes specific records.
+.TP
+drop
+Deletes entire fields.
+.TP
+index
+Adds a numeric index field.
+.TP
+rename
+Renames fields.
+.TP
+select
+Selects specific records.
+.TP
+sort
+Sorts records by field values.
+.TP
+update
+Updates field and value pairs.
+.TP
+merge
+Merges files.
+.TP
+split
+Splits database files by field values.
+.SS "output files:"
+.IP
+sequences
+.IP
+FASTA formatted sequences output from the subcommands fasta and clip.
+.IP
+<field>\-<value>
+.IP
+database files partitioned by annotation <field> and <value>.
+.IP
+parse\-<command>
+.IP
+output of the database modification functions where <command> is one of
+the subcommands add, index, drop, delete, rename, select, sort or update..
+.SS "required fields:"
+.IP
+sequence_id
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+changeo (1.0.1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * debhelper-compat 13 (routine-update)
+ * Set upstream metadata fields: Repository.
+ * Add manpages
+
+ -- Nilesh Patra <npatra974 at gmail.com> Thu, 15 Oct 2020 13:05:52 +0000
+
changeo (1.0.0-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <moeller at debian.org>
Section: science
Testsuite: autopkgtest-pkg-python
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all,
python3-setuptools
@@ -21,7 +21,7 @@ Depends: ${python3:Depends},
Recommends: python3-biopython (>=1.65),
python3-pandas (>= 0.15),
python3-scipy,
- python3-presto,
+ python3-presto (>= 0.6.2),
python3-airr
Description: Repertoire clonal assignment toolkit (Python 3)
Change-O is a collection of tools for processing the output of V(D)J
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,127 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=AlignRecords.py
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+progname=AssignGenes.py
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+progname=BuildTrees.py
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+progname=ConvertDb.py
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+progname=CreateGermlines.py
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+progname=DefineClones.py
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+progname=MakeDb.py
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+progname=ParseDb.py
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/rules
=====================================
@@ -5,3 +5,7 @@ export PYBUILD_NAME=changeo
%:
dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_installman:
+ # Trick to avoid manpage to assume files with extension .py is a language
+ dh_installman --language=C
=====================================
debian/upstream/metadata
=====================================
@@ -23,3 +23,4 @@ Registry:
Entry: NA
- Name: conda:bioconda
Entry: changeo
+Repository: https://bitbucket.org/kleinstein/changeo
=====================================
requirements.txt
=====================================
@@ -1,8 +1,8 @@
numpy>=1.8
scipy>=0.14
pandas>=0.24
-biopython>=1.65
+biopython>=1.71
PyYAML>=3.12
setuptools>=2.0
-presto>=0.5.10
+presto>=0.6.2
airr>=1.2.1
View it on GitLab: https://salsa.debian.org/med-team/changeo/-/compare/e0e3ae62119eb8b6a35812e2d315f9dd35928fa2...902f953af73bbad62558ca6142e97ed7f9a3e547
--
View it on GitLab: https://salsa.debian.org/med-team/changeo/-/compare/e0e3ae62119eb8b6a35812e2d315f9dd35928fa2...902f953af73bbad62558ca6142e97ed7f9a3e547
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